Starting phenix.real_space_refine on Tue Mar 3 14:04:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f3t_31440/03_2026/7f3t_31440.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f3t_31440/03_2026/7f3t_31440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f3t_31440/03_2026/7f3t_31440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f3t_31440/03_2026/7f3t_31440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f3t_31440/03_2026/7f3t_31440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f3t_31440/03_2026/7f3t_31440.map" } resolution = 3.69 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= 0.003 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 34 5.16 5 C 3682 2.51 5 N 934 2.21 5 O 976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5632 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2768 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 8, 'TRANS': 321} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 1.85, per 1000 atoms: 0.33 Number of scatterers: 5632 At special positions: 0 Unit cell: (86.67, 118.77, 93.09, 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 P 6 15.00 O 976 8.00 N 934 7.00 C 3682 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: 0.51 Conformation dependent library (CDL) restraints added in 269.9 milliseconds 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1252 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 8 through 69 removed outlier: 3.558A pdb=" N CYS A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 99 removed outlier: 5.171A pdb=" N ALA A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 123 through 154 removed outlier: 4.440A pdb=" N TYR A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 186 removed outlier: 3.954A pdb=" N CYS A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 209 removed outlier: 4.289A pdb=" N HIS A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 253 removed outlier: 3.808A pdb=" N TYR A 239 " --> pdb=" O PHE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 299 removed outlier: 3.791A pdb=" N PHE A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Proline residue: A 277 - end of helix removed outlier: 3.702A pdb=" N ASP A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 336 removed outlier: 3.704A pdb=" N MET A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 8 through 69 removed outlier: 3.559A pdb=" N CYS B 12 " --> pdb=" O PRO B 8 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 99 removed outlier: 5.171A pdb=" N ALA B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 123 through 154 removed outlier: 4.440A pdb=" N TYR B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 186 removed outlier: 3.954A pdb=" N CYS B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 209 removed outlier: 4.288A pdb=" N HIS B 197 " --> pdb=" O TRP B 193 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 253 removed outlier: 3.808A pdb=" N TYR B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 299 removed outlier: 3.791A pdb=" N PHE B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Proline residue: B 277 - end of helix removed outlier: 3.702A pdb=" N ASP B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 336 removed outlier: 3.704A pdb=" N MET B 309 " --> pdb=" O TRP B 305 " (cutoff:3.500A) Proline residue: B 313 - end of helix 444 hydrogen bonds defined for protein. 1320 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: 0.83 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1595 1.33 - 1.45: 1148 1.45 - 1.57: 2989 1.57 - 1.69: 10 1.69 - 1.81: 50 Bond restraints: 5792 Sorted by residual: bond pdb=" O3B COA B1000 " pdb=" P3B COA B1000 " ideal model delta sigma weight residual 1.683 1.600 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O3B COA A1000 " pdb=" P3B COA A1000 " ideal model delta sigma weight residual 1.683 1.601 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C4A COA A1000 " pdb=" C5A COA A1000 " ideal model delta sigma weight residual 1.395 1.468 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C4A COA B1000 " pdb=" C5A COA B1000 " ideal model delta sigma weight residual 1.395 1.467 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C4A COA A1000 " pdb=" N9A COA A1000 " ideal model delta sigma weight residual 1.381 1.317 0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 5787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 7533 2.84 - 5.68: 259 5.68 - 8.52: 38 8.52 - 11.36: 10 11.36 - 14.20: 2 Bond angle restraints: 7842 Sorted by residual: angle pdb=" C GLN A 81 " pdb=" N GLU A 82 " pdb=" CA GLU A 82 " ideal model delta sigma weight residual 120.72 110.57 10.15 1.67e+00 3.59e-01 3.69e+01 angle pdb=" C GLN B 81 " pdb=" N GLU B 82 " pdb=" CA GLU B 82 " ideal model delta sigma weight residual 120.72 110.59 10.13 1.67e+00 3.59e-01 3.68e+01 angle pdb=" C LEU A 154 " pdb=" N LEU A 155 " pdb=" CA LEU A 155 " ideal model delta sigma weight residual 121.54 131.46 -9.92 1.91e+00 2.74e-01 2.70e+01 angle pdb=" C LEU B 154 " pdb=" N LEU B 155 " pdb=" CA LEU B 155 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.66e+01 angle pdb=" P1A COA A1000 " pdb=" O3A COA A1000 " pdb=" P2A COA A1000 " ideal model delta sigma weight residual 135.11 120.91 14.20 3.00e+00 1.11e-01 2.24e+01 ... (remaining 7837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2930 17.34 - 34.68: 364 34.68 - 52.02: 106 52.02 - 69.36: 22 69.36 - 86.70: 6 Dihedral angle restraints: 3428 sinusoidal: 1488 harmonic: 1940 Sorted by residual: dihedral pdb=" CA ILE A 189 " pdb=" C ILE A 189 " pdb=" N LYS A 190 " pdb=" CA LYS A 190 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ILE B 189 " pdb=" C ILE B 189 " pdb=" N LYS B 190 " pdb=" CA LYS B 190 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA LEU A 154 " pdb=" C LEU A 154 " pdb=" N LEU A 155 " pdb=" CA LEU A 155 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 3425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 591 0.057 - 0.114: 182 0.114 - 0.171: 41 0.171 - 0.228: 12 0.228 - 0.284: 2 Chirality restraints: 828 Sorted by residual: chirality pdb=" C2B COA B1000 " pdb=" C1B COA B1000 " pdb=" C3B COA B1000 " pdb=" O2B COA B1000 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2B COA A1000 " pdb=" C1B COA A1000 " pdb=" C3B COA A1000 " pdb=" O2B COA A1000 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ARG A 14 " pdb=" N ARG A 14 " pdb=" C ARG A 14 " pdb=" CB ARG A 14 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 825 not shown) Planarity restraints: 966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P COA B1000 " -0.308 2.00e-02 2.50e+03 2.56e-01 8.19e+02 pdb=" C9P COA B1000 " 0.094 2.00e-02 2.50e+03 pdb=" CAP COA B1000 " -0.201 2.00e-02 2.50e+03 pdb=" N8P COA B1000 " 0.428 2.00e-02 2.50e+03 pdb=" O9P COA B1000 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P COA A1000 " 0.308 2.00e-02 2.50e+03 2.56e-01 8.18e+02 pdb=" C9P COA A1000 " -0.094 2.00e-02 2.50e+03 pdb=" CAP COA A1000 " 0.201 2.00e-02 2.50e+03 pdb=" N8P COA A1000 " -0.428 2.00e-02 2.50e+03 pdb=" O9P COA A1000 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P COA B1000 " -0.038 2.00e-02 2.50e+03 3.07e-02 1.18e+01 pdb=" C5P COA B1000 " 0.009 2.00e-02 2.50e+03 pdb=" C6P COA B1000 " -0.028 2.00e-02 2.50e+03 pdb=" N4P COA B1000 " 0.049 2.00e-02 2.50e+03 pdb=" O5P COA B1000 " 0.008 2.00e-02 2.50e+03 ... (remaining 963 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 185 2.68 - 3.23: 5977 3.23 - 3.79: 8941 3.79 - 4.34: 10341 4.34 - 4.90: 17071 Nonbonded interactions: 42515 Sorted by model distance: nonbonded pdb=" NE2 GLN A 54 " pdb=" OD2 ASP B 22 " model vdw 2.124 3.120 nonbonded pdb=" OD2 ASP A 22 " pdb=" NE2 GLN B 54 " model vdw 2.155 3.120 nonbonded pdb=" NH1 ARG B 57 " pdb=" OE2 GLU B 60 " model vdw 2.221 3.120 nonbonded pdb=" NH1 ARG A 57 " pdb=" OE2 GLU A 60 " model vdw 2.221 3.120 nonbonded pdb=" O LEU B 83 " pdb=" NE2 GLN B 86 " model vdw 2.235 3.120 ... (remaining 42510 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.89 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.083 5792 Z= 0.476 Angle : 1.227 14.197 7842 Z= 0.637 Chirality : 0.060 0.284 828 Planarity : 0.013 0.256 966 Dihedral : 16.921 86.699 2176 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.18 % Favored : 94.51 % Rotamer: Outliers : 0.33 % Allowed : 2.51 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.32), residues: 656 helix: 0.98 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.50 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 14 TYR 0.024 0.002 TYR B 171 PHE 0.019 0.002 PHE A 274 TRP 0.015 0.002 TRP B 192 HIS 0.007 0.002 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.01100 ( 5792) covalent geometry : angle 1.22744 ( 7842) hydrogen bonds : bond 0.11462 ( 444) hydrogen bonds : angle 5.71364 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.212 Fit side-chains REVERT: A 309 MET cc_start: 0.8572 (mmm) cc_final: 0.8286 (mmt) REVERT: B 309 MET cc_start: 0.8570 (mmm) cc_final: 0.8309 (mmt) outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.0620 time to fit residues: 6.2457 Evaluate side-chains 61 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.152254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117704 restraints weight = 7856.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117841 restraints weight = 9114.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118865 restraints weight = 7619.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118976 restraints weight = 5220.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119549 restraints weight = 4963.323| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5792 Z= 0.155 Angle : 0.725 9.254 7842 Z= 0.377 Chirality : 0.040 0.146 828 Planarity : 0.004 0.029 966 Dihedral : 10.387 56.091 840 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.51 % Allowed : 12.04 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.34), residues: 656 helix: 2.25 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -1.36 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 14 TYR 0.016 0.001 TYR A 238 PHE 0.010 0.001 PHE A 127 TRP 0.016 0.001 TRP A 192 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5792) covalent geometry : angle 0.72482 ( 7842) hydrogen bonds : bond 0.06763 ( 444) hydrogen bonds : angle 4.17763 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.219 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 98 average time/residue: 0.0691 time to fit residues: 9.1807 Evaluate side-chains 72 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 302 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 0.0670 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.148429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113298 restraints weight = 7831.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113482 restraints weight = 9536.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114530 restraints weight = 7952.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114516 restraints weight = 5352.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115218 restraints weight = 5066.310| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5792 Z= 0.170 Angle : 0.711 9.626 7842 Z= 0.367 Chirality : 0.041 0.144 828 Planarity : 0.004 0.028 966 Dihedral : 8.890 47.701 840 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.85 % Allowed : 14.88 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.34), residues: 656 helix: 2.48 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.35 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 14 TYR 0.016 0.001 TYR A 171 PHE 0.008 0.001 PHE A 127 TRP 0.012 0.001 TRP B 192 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5792) covalent geometry : angle 0.71102 ( 7842) hydrogen bonds : bond 0.06809 ( 444) hydrogen bonds : angle 4.06656 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 120 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6853 (tt) REVERT: B 212 ASP cc_start: 0.8354 (p0) cc_final: 0.8061 (p0) REVERT: B 215 MET cc_start: 0.7205 (tmm) cc_final: 0.6994 (tmm) outliers start: 23 outliers final: 12 residues processed: 86 average time/residue: 0.0661 time to fit residues: 7.7276 Evaluate side-chains 81 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 328 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.151015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.115715 restraints weight = 7846.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115996 restraints weight = 9333.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117109 restraints weight = 7570.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117276 restraints weight = 5104.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117881 restraints weight = 5023.243| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5792 Z= 0.148 Angle : 0.676 10.380 7842 Z= 0.347 Chirality : 0.039 0.145 828 Planarity : 0.004 0.026 966 Dihedral : 8.216 46.916 840 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.18 % Allowed : 17.39 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.34), residues: 656 helix: 2.71 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.29 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 14 TYR 0.012 0.001 TYR A 171 PHE 0.007 0.001 PHE A 127 TRP 0.011 0.001 TRP A 192 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5792) covalent geometry : angle 0.67641 ( 7842) hydrogen bonds : bond 0.06139 ( 444) hydrogen bonds : angle 3.91857 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 CYS cc_start: 0.7552 (m) cc_final: 0.7201 (m) REVERT: B 151 CYS cc_start: 0.7619 (m) cc_final: 0.7347 (m) REVERT: B 212 ASP cc_start: 0.8370 (p0) cc_final: 0.8101 (p0) outliers start: 25 outliers final: 15 residues processed: 93 average time/residue: 0.0517 time to fit residues: 7.1450 Evaluate side-chains 88 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 302 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.149357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114045 restraints weight = 7901.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114364 restraints weight = 9004.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114851 restraints weight = 8144.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115252 restraints weight = 5421.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115747 restraints weight = 5000.844| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5792 Z= 0.159 Angle : 0.683 10.618 7842 Z= 0.348 Chirality : 0.039 0.140 828 Planarity : 0.003 0.024 966 Dihedral : 8.093 51.207 840 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.51 % Allowed : 20.74 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.34), residues: 656 helix: 2.63 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.69 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 178 TYR 0.015 0.001 TYR A 171 PHE 0.009 0.001 PHE B 136 TRP 0.011 0.001 TRP A 192 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 5792) covalent geometry : angle 0.68304 ( 7842) hydrogen bonds : bond 0.06201 ( 444) hydrogen bonds : angle 3.90884 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 276 LEU cc_start: 0.8628 (tp) cc_final: 0.8294 (tp) REVERT: B 212 ASP cc_start: 0.8322 (p0) cc_final: 0.8102 (p0) REVERT: B 215 MET cc_start: 0.7409 (tmm) cc_final: 0.7153 (tmm) outliers start: 21 outliers final: 14 residues processed: 82 average time/residue: 0.0557 time to fit residues: 6.7282 Evaluate side-chains 82 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 328 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.147367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111182 restraints weight = 7913.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110732 restraints weight = 7676.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112313 restraints weight = 5940.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112652 restraints weight = 3991.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112719 restraints weight = 3876.208| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5792 Z= 0.153 Angle : 0.678 11.114 7842 Z= 0.345 Chirality : 0.039 0.154 828 Planarity : 0.003 0.024 966 Dihedral : 8.016 53.394 840 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.01 % Allowed : 20.57 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.34), residues: 656 helix: 2.66 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.53 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 178 TYR 0.014 0.001 TYR A 171 PHE 0.011 0.001 PHE B 127 TRP 0.011 0.001 TRP A 192 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5792) covalent geometry : angle 0.67764 ( 7842) hydrogen bonds : bond 0.05983 ( 444) hydrogen bonds : angle 3.89534 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 LEU cc_start: 0.8655 (tp) cc_final: 0.8326 (tp) REVERT: A 285 TRP cc_start: 0.8657 (t-100) cc_final: 0.8390 (t60) REVERT: B 212 ASP cc_start: 0.8350 (p0) cc_final: 0.8146 (p0) REVERT: B 215 MET cc_start: 0.7587 (tmm) cc_final: 0.7386 (tmm) REVERT: B 269 TRP cc_start: 0.7976 (m100) cc_final: 0.7576 (m100) REVERT: B 276 LEU cc_start: 0.8649 (tp) cc_final: 0.8298 (tp) outliers start: 24 outliers final: 19 residues processed: 86 average time/residue: 0.0506 time to fit residues: 6.5519 Evaluate side-chains 84 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 328 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.146766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110863 restraints weight = 8016.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109449 restraints weight = 7553.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.110946 restraints weight = 5938.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.111110 restraints weight = 4152.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111206 restraints weight = 4252.837| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5792 Z= 0.164 Angle : 0.736 14.796 7842 Z= 0.372 Chirality : 0.040 0.203 828 Planarity : 0.003 0.022 966 Dihedral : 7.992 54.687 840 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.35 % Allowed : 21.24 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.34), residues: 656 helix: 2.66 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.50 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.015 0.001 TYR B 171 PHE 0.009 0.001 PHE A 136 TRP 0.011 0.001 TRP B 285 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5792) covalent geometry : angle 0.73567 ( 7842) hydrogen bonds : bond 0.06118 ( 444) hydrogen bonds : angle 3.98595 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 LEU cc_start: 0.8667 (tp) cc_final: 0.8330 (tp) REVERT: A 285 TRP cc_start: 0.8678 (t-100) cc_final: 0.8372 (t60) REVERT: B 276 LEU cc_start: 0.8679 (tp) cc_final: 0.8336 (tp) REVERT: B 285 TRP cc_start: 0.8655 (t-100) cc_final: 0.8340 (t60) outliers start: 26 outliers final: 22 residues processed: 87 average time/residue: 0.0521 time to fit residues: 6.7140 Evaluate side-chains 88 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.148403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113433 restraints weight = 7817.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108855 restraints weight = 6662.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110103 restraints weight = 8049.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110869 restraints weight = 5132.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111277 restraints weight = 4504.568| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5792 Z= 0.154 Angle : 0.735 13.096 7842 Z= 0.372 Chirality : 0.039 0.147 828 Planarity : 0.003 0.024 966 Dihedral : 7.866 55.860 840 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.01 % Allowed : 22.74 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.34), residues: 656 helix: 2.76 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.53 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 31 TYR 0.013 0.001 TYR B 239 PHE 0.008 0.001 PHE B 127 TRP 0.011 0.001 TRP B 192 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5792) covalent geometry : angle 0.73506 ( 7842) hydrogen bonds : bond 0.05747 ( 444) hydrogen bonds : angle 3.91056 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.7718 (ttm) cc_final: 0.7392 (mtt) REVERT: A 276 LEU cc_start: 0.8660 (tp) cc_final: 0.8336 (tp) REVERT: A 285 TRP cc_start: 0.8647 (t-100) cc_final: 0.8343 (t60) REVERT: B 179 GLU cc_start: 0.8449 (pt0) cc_final: 0.8174 (mt-10) REVERT: B 276 LEU cc_start: 0.8673 (tp) cc_final: 0.8349 (tp) REVERT: B 285 TRP cc_start: 0.8650 (t-100) cc_final: 0.8337 (t60) outliers start: 24 outliers final: 19 residues processed: 85 average time/residue: 0.0511 time to fit residues: 6.4703 Evaluate side-chains 85 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.0070 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.153504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119883 restraints weight = 7670.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116383 restraints weight = 6763.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117481 restraints weight = 7656.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118367 restraints weight = 4693.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118497 restraints weight = 4059.698| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5792 Z= 0.153 Angle : 0.742 13.215 7842 Z= 0.372 Chirality : 0.040 0.175 828 Planarity : 0.003 0.023 966 Dihedral : 7.775 56.371 840 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.18 % Allowed : 23.41 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.34), residues: 656 helix: 2.78 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.56 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TYR 0.012 0.001 TYR B 171 PHE 0.010 0.001 PHE A 23 TRP 0.012 0.001 TRP A 192 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5792) covalent geometry : angle 0.74248 ( 7842) hydrogen bonds : bond 0.05625 ( 444) hydrogen bonds : angle 3.91644 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7984 (t80) cc_final: 0.7433 (m-80) REVERT: A 228 MET cc_start: 0.7733 (ttm) cc_final: 0.7412 (mtt) REVERT: A 276 LEU cc_start: 0.8603 (tp) cc_final: 0.8294 (tp) REVERT: A 285 TRP cc_start: 0.8622 (t-100) cc_final: 0.8334 (t60) REVERT: B 23 PHE cc_start: 0.8100 (t80) cc_final: 0.7783 (t80) REVERT: B 179 GLU cc_start: 0.8422 (pt0) cc_final: 0.8198 (mt-10) REVERT: B 276 LEU cc_start: 0.8617 (tp) cc_final: 0.8300 (tp) REVERT: B 285 TRP cc_start: 0.8618 (t-100) cc_final: 0.8325 (t60) outliers start: 19 outliers final: 17 residues processed: 83 average time/residue: 0.0490 time to fit residues: 6.1071 Evaluate side-chains 87 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.151314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116283 restraints weight = 7847.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112996 restraints weight = 8352.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115078 restraints weight = 7725.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115274 restraints weight = 5070.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115479 restraints weight = 4693.522| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 5792 Z= 0.177 Angle : 0.785 13.251 7842 Z= 0.400 Chirality : 0.041 0.221 828 Planarity : 0.003 0.022 966 Dihedral : 7.883 56.575 840 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.18 % Allowed : 23.58 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.34), residues: 656 helix: 2.71 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.55 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 14 TYR 0.016 0.001 TYR B 171 PHE 0.009 0.001 PHE A 23 TRP 0.012 0.001 TRP B 285 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5792) covalent geometry : angle 0.78530 ( 7842) hydrogen bonds : bond 0.06037 ( 444) hydrogen bonds : angle 4.03451 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.8011 (t80) cc_final: 0.7498 (m-80) REVERT: A 228 MET cc_start: 0.7849 (ttm) cc_final: 0.7523 (mtt) REVERT: A 276 LEU cc_start: 0.8636 (tp) cc_final: 0.8316 (tp) REVERT: B 276 LEU cc_start: 0.8643 (tp) cc_final: 0.8318 (tp) outliers start: 19 outliers final: 19 residues processed: 81 average time/residue: 0.0486 time to fit residues: 5.9939 Evaluate side-chains 83 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.117654 restraints weight = 7635.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116990 restraints weight = 8088.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118295 restraints weight = 6955.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118435 restraints weight = 4520.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118513 restraints weight = 4286.723| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 5792 Z= 0.164 Angle : 0.774 13.096 7842 Z= 0.395 Chirality : 0.041 0.237 828 Planarity : 0.003 0.023 966 Dihedral : 7.829 57.374 840 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.51 % Allowed : 23.41 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.34), residues: 656 helix: 2.74 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.57 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 178 TYR 0.013 0.001 TYR A 171 PHE 0.008 0.001 PHE A 127 TRP 0.012 0.001 TRP A 192 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5792) covalent geometry : angle 0.77424 ( 7842) hydrogen bonds : bond 0.05725 ( 444) hydrogen bonds : angle 3.96970 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 912.51 seconds wall clock time: 16 minutes 20.87 seconds (980.87 seconds total)