Starting phenix.real_space_refine on Fri Aug 22 16:59:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j2f_35948/08_2025/8j2f_35948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j2f_35948/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j2f_35948/08_2025/8j2f_35948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j2f_35948/08_2025/8j2f_35948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j2f_35948/08_2025/8j2f_35948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j2f_35948/08_2025/8j2f_35948.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.99, per 1000 atoms: 0.32 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: 0.42 Conformation dependent library (CDL) restraints added in 315.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.12 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: 0.63 Time building geometry restraints manager: 0.55 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: 0.01 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: 0.690 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.180 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.040 ------------------------------------------------------------------------------- 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= 0.404 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG B 8 TYR 0.013 0.002 TYR B 105 PHE 0.015 0.002 PHE B 371 TRP 0.010 0.001 TRP B 310 HIS 0.007 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 6334) covalent geometry : angle 1.21241 ( 8582) hydrogen bonds : bond 0.15916 ( 362) hydrogen bonds : angle 5.33875 ( 1044) *********************** 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 : 0.236 Fit side-chains revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7764 (m-30) cc_final: 0.6965 (m-30) REVERT: A 383 TYR cc_start: 0.7201 (t80) cc_final: 0.6797 (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: 0.7752 (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: 0.7123 (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: 0.1050 time to fit residues: 18.7431 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 : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 50.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.138187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.096019 restraints weight = 6999.083| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.09 r_work: 0.2780 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6334 Z= 0.147 Angle : 0.527 5.901 8582 Z= 0.284 Chirality : 0.042 0.189 920 Planarity : 0.004 0.032 1082 Dihedral : 5.300 41.571 862 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.72 % Allowed : 8.31 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.09 (0.31), residues: 760 helix: 4.29 (0.26), residues: 322 sheet: 1.67 (0.34), residues: 174 loop : -0.75 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 8 TYR 0.008 0.001 TYR A 141 PHE 0.018 0.001 PHE A 371 TRP 0.011 0.001 TRP A 17 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6334) covalent geometry : angle 0.52687 ( 8582) hydrogen bonds : bond 0.05361 ( 362) hydrogen bonds : angle 4.11927 ( 1044) *********************** 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 99 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 383 TYR cc_start: 0.8196 (t80) cc_final: 0.7762 (t80) REVERT: B 61 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7832 (tm-30) REVERT: B 145 LYS cc_start: 0.6990 (tttt) cc_final: 0.6660 (tttm) REVERT: B 184 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: B 253 LYS cc_start: 0.7769 (tptt) cc_final: 0.7267 (tttm) REVERT: B 383 TYR cc_start: 0.8169 (t80) cc_final: 0.7709 (t80) outliers start: 11 outliers final: 3 residues processed: 96 average time/residue: 0.1182 time to fit residues: 13.8941 Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.089199 restraints weight = 6926.407| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.11 r_work: 0.2725 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 6334 Z= 0.194 Angle : 0.556 7.648 8582 Z= 0.296 Chirality : 0.043 0.182 920 Planarity : 0.004 0.032 1082 Dihedral : 5.663 48.108 862 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.72 % Allowed : 8.78 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.31), residues: 760 helix: 4.13 (0.27), residues: 318 sheet: 1.53 (0.35), residues: 174 loop : -0.66 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 384 TYR 0.009 0.001 TYR A 105 PHE 0.014 0.002 PHE A 371 TRP 0.012 0.002 TRP A 17 HIS 0.006 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 6334) covalent geometry : angle 0.55634 ( 8582) hydrogen bonds : bond 0.05412 ( 362) hydrogen bonds : angle 4.07636 ( 1044) *********************** 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 96 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7575 (ttpp) cc_final: 0.7124 (tptp) REVERT: A 383 TYR cc_start: 0.8321 (t80) cc_final: 0.7981 (t80) REVERT: B 30 MET cc_start: 0.8237 (mmt) cc_final: 0.7901 (mmp) REVERT: B 145 LYS cc_start: 0.7323 (tttt) cc_final: 0.7096 (tttm) REVERT: B 184 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: B 383 TYR cc_start: 0.8336 (t80) cc_final: 0.8000 (t80) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.1026 time to fit residues: 11.8803 Evaluate side-chains 86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 87 LYS Chi-restraints excluded: chain A residue 99 THR 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 169 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 29 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 0.0020 overall best weight: 1.9394 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.127222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.084324 restraints weight = 6990.991| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.15 r_work: 0.2639 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3660 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= 0.193 Angle : 0.539 7.485 8582 Z= 0.285 Chirality : 0.042 0.143 920 Planarity : 0.004 0.033 1082 Dihedral : 5.667 48.723 862 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.31), residues: 760 helix: 3.93 (0.27), residues: 318 sheet: 1.30 (0.36), residues: 174 loop : -0.76 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 8 TYR 0.008 0.001 TYR A 105 PHE 0.015 0.001 PHE A 371 TRP 0.009 0.001 TRP A 17 HIS 0.005 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 6334) covalent geometry : angle 0.53916 ( 8582) hydrogen bonds : bond 0.05142 ( 362) hydrogen bonds : angle 3.97963 ( 1044) *********************** 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: 12 poor density : 79 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7631 (ttpp) cc_final: 0.7151 (tptp) REVERT: A 383 TYR cc_start: 0.8357 (t80) cc_final: 0.8027 (t80) REVERT: B 30 MET cc_start: 0.8207 (mmt) cc_final: 0.7957 (mmp) REVERT: B 145 LYS cc_start: 0.7511 (tttt) cc_final: 0.7287 (tttm) REVERT: B 184 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: B 383 TYR cc_start: 0.8314 (t80) cc_final: 0.7966 (t80) outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 0.1061 time to fit residues: 11.1209 Evaluate side-chains 84 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.137731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.095974 restraints weight = 6980.369| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.11 r_work: 0.2739 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6334 Z= 0.100 Angle : 0.452 9.711 8582 Z= 0.237 Chirality : 0.038 0.136 920 Planarity : 0.003 0.031 1082 Dihedral : 5.219 56.127 862 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.10 % Allowed : 11.76 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.31), residues: 760 helix: 4.30 (0.27), residues: 318 sheet: 1.27 (0.36), residues: 174 loop : -0.66 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 8 TYR 0.005 0.001 TYR A 105 PHE 0.012 0.001 PHE B 371 TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 6334) covalent geometry : angle 0.45232 ( 8582) hydrogen bonds : bond 0.04032 ( 362) hydrogen bonds : angle 3.68878 ( 1044) *********************** 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 93 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7477 (tttp) REVERT: A 383 TYR cc_start: 0.8224 (t80) cc_final: 0.7969 (t80) REVERT: B 184 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7955 (pm20) REVERT: B 383 TYR cc_start: 0.8194 (t80) cc_final: 0.7906 (t80) outliers start: 7 outliers final: 2 residues processed: 90 average time/residue: 0.0994 time to fit residues: 11.2301 Evaluate side-chains 76 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 184 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 33 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.124756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.081746 restraints weight = 7014.760| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.15 r_work: 0.2686 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 6334 Z= 0.262 Angle : 0.597 8.796 8582 Z= 0.307 Chirality : 0.044 0.140 920 Planarity : 0.004 0.039 1082 Dihedral : 5.830 46.827 862 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.31), residues: 760 helix: 3.65 (0.28), residues: 322 sheet: 1.13 (0.36), residues: 174 loop : -0.85 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 10 TYR 0.007 0.001 TYR B 98 PHE 0.017 0.002 PHE B 371 TRP 0.009 0.002 TRP A 17 HIS 0.006 0.002 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 6334) covalent geometry : angle 0.59702 ( 8582) hydrogen bonds : bond 0.05447 ( 362) hydrogen bonds : angle 4.04903 ( 1044) *********************** 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 86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7281 (tptp) REVERT: A 307 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7630 (ttmt) REVERT: A 383 TYR cc_start: 0.8403 (t80) cc_final: 0.8120 (t80) REVERT: B 184 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: B 253 LYS cc_start: 0.7925 (tptt) cc_final: 0.7326 (tttm) REVERT: B 383 TYR cc_start: 0.8344 (t80) cc_final: 0.8048 (t80) outliers start: 14 outliers final: 6 residues processed: 80 average time/residue: 0.1240 time to fit residues: 12.2423 Evaluate side-chains 78 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 184 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 33 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.128715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.086032 restraints weight = 6928.335| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.15 r_work: 0.2768 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6334 Z= 0.122 Angle : 0.482 8.979 8582 Z= 0.248 Chirality : 0.039 0.137 920 Planarity : 0.003 0.038 1082 Dihedral : 5.351 51.103 862 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.57 % Allowed : 12.70 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.31), residues: 760 helix: 3.98 (0.28), residues: 322 sheet: 1.06 (0.36), residues: 174 loop : -0.82 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 8 TYR 0.005 0.001 TYR A 105 PHE 0.012 0.001 PHE B 371 TRP 0.007 0.001 TRP A 310 HIS 0.004 0.001 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6334) covalent geometry : angle 0.48185 ( 8582) hydrogen bonds : bond 0.04351 ( 362) hydrogen bonds : angle 3.78574 ( 1044) *********************** 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 79 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7379 (tptp) REVERT: A 307 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7603 (ttmt) REVERT: A 383 TYR cc_start: 0.8290 (t80) cc_final: 0.8036 (t80) REVERT: B 303 MET cc_start: 0.7190 (mmt) cc_final: 0.6925 (mmt) REVERT: B 383 TYR cc_start: 0.8251 (t80) cc_final: 0.7980 (t80) outliers start: 10 outliers final: 5 residues processed: 77 average time/residue: 0.1127 time to fit residues: 10.8651 Evaluate side-chains 75 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 169 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 63 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.124417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.081215 restraints weight = 7139.671| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.17 r_work: 0.2614 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 6334 Z= 0.264 Angle : 0.597 8.658 8582 Z= 0.306 Chirality : 0.044 0.142 920 Planarity : 0.004 0.043 1082 Dihedral : 5.824 46.445 862 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.04 % Allowed : 11.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.31), residues: 760 helix: 3.60 (0.28), residues: 322 sheet: 0.96 (0.37), residues: 174 loop : -0.97 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 10 TYR 0.006 0.001 TYR B 383 PHE 0.017 0.002 PHE B 371 TRP 0.009 0.001 TRP B 17 HIS 0.006 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00642 ( 6334) covalent geometry : angle 0.59657 ( 8582) hydrogen bonds : bond 0.05426 ( 362) hydrogen bonds : angle 4.04996 ( 1044) *********************** 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 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7365 (tptp) REVERT: A 307 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7569 (ttmt) REVERT: A 383 TYR cc_start: 0.8435 (t80) cc_final: 0.8149 (t80) REVERT: B 253 LYS cc_start: 0.7920 (tptt) cc_final: 0.7313 (tttm) REVERT: B 383 TYR cc_start: 0.8371 (t80) cc_final: 0.8044 (t80) outliers start: 13 outliers final: 7 residues processed: 79 average time/residue: 0.1171 time to fit residues: 11.4174 Evaluate side-chains 79 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 359 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 169 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.130189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.087556 restraints weight = 6991.207| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.16 r_work: 0.2707 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4117 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= 0.104 Angle : 0.462 8.116 8582 Z= 0.239 Chirality : 0.038 0.135 920 Planarity : 0.003 0.038 1082 Dihedral : 5.199 54.585 862 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.88 % Allowed : 12.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.31), residues: 760 helix: 4.03 (0.28), residues: 322 sheet: 0.92 (0.36), residues: 174 loop : -0.88 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 8 TYR 0.004 0.001 TYR A 383 PHE 0.013 0.001 PHE B 371 TRP 0.008 0.001 TRP A 310 HIS 0.004 0.001 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 6334) covalent geometry : angle 0.46185 ( 8582) hydrogen bonds : bond 0.04019 ( 362) hydrogen bonds : angle 3.70164 ( 1044) *********************** 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 82 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7509 (tptp) REVERT: A 307 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7533 (ttmt) REVERT: A 383 TYR cc_start: 0.8276 (t80) cc_final: 0.7998 (t80) REVERT: B 307 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7737 (ttmt) REVERT: B 383 TYR cc_start: 0.8208 (t80) cc_final: 0.7909 (t80) outliers start: 12 outliers final: 6 residues processed: 79 average time/residue: 0.1016 time to fit residues: 10.2282 Evaluate side-chains 76 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 307 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.134924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.093352 restraints weight = 6912.371| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.09 r_work: 0.2808 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6334 Z= 0.104 Angle : 0.466 9.447 8582 Z= 0.237 Chirality : 0.038 0.133 920 Planarity : 0.003 0.035 1082 Dihedral : 5.128 57.734 862 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.57 % Allowed : 12.70 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.32), residues: 760 helix: 4.25 (0.27), residues: 318 sheet: 0.92 (0.36), residues: 174 loop : -0.83 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 8 TYR 0.005 0.001 TYR A 105 PHE 0.011 0.001 PHE A 371 TRP 0.006 0.001 TRP B 358 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 6334) covalent geometry : angle 0.46572 ( 8582) hydrogen bonds : bond 0.03879 ( 362) hydrogen bonds : angle 3.62593 ( 1044) ********************** 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 77 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7471 (tptp) REVERT: A 383 TYR cc_start: 0.8249 (t80) cc_final: 0.8021 (t80) REVERT: B 307 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7765 (ttmt) REVERT: B 383 TYR cc_start: 0.8227 (t80) cc_final: 0.7963 (t80) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.1067 time to fit residues: 10.1856 Evaluate side-chains 75 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 169 LYS Chi-restraints excluded: chain B residue 307 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.125853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.082933 restraints weight = 6989.344| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.17 r_work: 0.2637 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 6334 Z= 0.196 Angle : 0.566 8.960 8582 Z= 0.285 Chirality : 0.042 0.178 920 Planarity : 0.004 0.040 1082 Dihedral : 5.576 49.829 862 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.51 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.31), residues: 760 helix: 3.80 (0.28), residues: 322 sheet: 0.93 (0.36), residues: 174 loop : -0.92 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 10 TYR 0.005 0.001 TYR B 383 PHE 0.011 0.001 PHE B 371 TRP 0.006 0.001 TRP B 310 HIS 0.005 0.001 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 6334) covalent geometry : angle 0.56607 ( 8582) hydrogen bonds : bond 0.04871 ( 362) hydrogen bonds : angle 3.93909 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1657.89 seconds wall clock time: 29 minutes 1.12 seconds (1741.12 seconds total)