Starting phenix.real_space_refine on Thu Jul 2 00:17:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ght_40050/07_2026/8ght_40050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ght_40050/07_2026/8ght_40050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ght_40050/07_2026/8ght_40050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ght_40050/07_2026/8ght_40050.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ght_40050/07_2026/8ght_40050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ght_40050/07_2026/8ght_40050.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ght_40050/07_2026/8ght_40050.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ght_40050/07_2026/8ght_40050.cif" } resolution = 3.05 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= 0.014 sd= 0.091 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: 6 Type Number sf(0) Gaussians Cd 6 9.23 5 P 2 5.49 5 S 24 5.16 5 C 2818 2.51 5 N 740 2.21 5 O 776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4366 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2139 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain: "B" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2139 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Ad-hoc single atom residues: {' CD': 3} Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Ad-hoc single atom residues: {' CD': 3} Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="CD CD B 503 " occ=0.60 Time building chain proxies: 1.04, per 1000 atoms: 0.24 Number of scatterers: 4366 At special positions: 0 Unit cell: (71.928, 83.916, 65.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cd 6 47.96 S 24 16.00 P 2 15.00 O 776 8.00 N 740 7.00 C 2818 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 110.4 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 88.7% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 6 through 22 removed outlier: 3.519A pdb=" N SER A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 50 Processing helix chain 'A' and resid 52 through 76 removed outlier: 3.677A pdb=" N VAL A 56 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.933A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 81' Processing helix chain 'A' and resid 84 through 120 removed outlier: 3.569A pdb=" N GLN A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 122 through 146 removed outlier: 4.194A pdb=" N ALA A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 189 removed outlier: 3.651A pdb=" N LEU A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 193 through 223 removed outlier: 4.193A pdb=" N GLY A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Proline residue: A 199 - end of helix Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 228 through 252 Proline residue: A 241 - end of helix removed outlier: 3.543A pdb=" N SER A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 278 removed outlier: 3.593A pdb=" N ILE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 309 removed outlier: 3.656A pdb=" N ALA A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.519A pdb=" N SER B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 Processing helix chain 'B' and resid 52 through 76 removed outlier: 3.677A pdb=" N VAL B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.932A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 81' Processing helix chain 'B' and resid 84 through 120 removed outlier: 3.569A pdb=" N GLN B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 122 through 146 removed outlier: 4.194A pdb=" N ALA B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 189 removed outlier: 3.652A pdb=" N LEU B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 193 through 223 removed outlier: 4.193A pdb=" N GLY B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Proline residue: B 199 - end of helix Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 228 through 252 Proline residue: B 241 - end of helix removed outlier: 3.542A pdb=" N SER B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 278 removed outlier: 3.593A pdb=" N ILE B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 309 removed outlier: 3.655A pdb=" N ALA B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA2, first strand: chain 'B' and resid 149 through 150 393 hydrogen bonds defined for protein. 1173 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: 0.68 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 702 1.31 - 1.43: 1056 1.43 - 1.56: 2626 1.56 - 1.68: 4 1.68 - 1.81: 48 Bond restraints: 4436 Sorted by residual: bond pdb=" C8 PTY B 501 " pdb=" O7 PTY B 501 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C8 PTY A 404 " pdb=" O7 PTY A 404 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C30 PTY A 404 " pdb=" O4 PTY A 404 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C30 PTY B 501 " pdb=" O4 PTY B 501 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C6 PTY B 501 " pdb=" O7 PTY B 501 " ideal model delta sigma weight residual 1.432 1.398 0.034 2.00e-02 2.50e+03 2.94e+00 ... (remaining 4431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 5948 3.30 - 6.61: 78 6.61 - 9.91: 6 9.91 - 13.22: 0 13.22 - 16.52: 2 Bond angle restraints: 6034 Sorted by residual: angle pdb=" O11 PTY A 404 " pdb=" P1 PTY A 404 " pdb=" O14 PTY A 404 " ideal model delta sigma weight residual 92.90 109.42 -16.52 3.00e+00 1.11e-01 3.03e+01 angle pdb=" O11 PTY B 501 " pdb=" P1 PTY B 501 " pdb=" O14 PTY B 501 " ideal model delta sigma weight residual 92.90 109.40 -16.50 3.00e+00 1.11e-01 3.02e+01 angle pdb=" N THR A 281 " pdb=" CA THR A 281 " pdb=" C THR A 281 " ideal model delta sigma weight residual 114.56 110.19 4.37 1.27e+00 6.20e-01 1.19e+01 angle pdb=" N THR B 281 " pdb=" CA THR B 281 " pdb=" C THR B 281 " ideal model delta sigma weight residual 114.56 110.19 4.37 1.27e+00 6.20e-01 1.18e+01 angle pdb=" O12 PTY A 404 " pdb=" P1 PTY A 404 " pdb=" O13 PTY A 404 " ideal model delta sigma weight residual 119.61 110.02 9.59 3.00e+00 1.11e-01 1.02e+01 ... (remaining 6029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.09: 2518 33.09 - 66.18: 54 66.18 - 99.27: 6 99.27 - 132.36: 0 132.36 - 165.45: 2 Dihedral angle restraints: 2580 sinusoidal: 916 harmonic: 1664 Sorted by residual: dihedral pdb=" CA ILE A 278 " pdb=" C ILE A 278 " pdb=" N PRO A 279 " pdb=" CA PRO A 279 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ILE B 278 " pdb=" C ILE B 278 " pdb=" N PRO B 279 " pdb=" CA PRO B 279 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" C3 PTY B 501 " pdb=" O11 PTY B 501 " pdb=" P1 PTY B 501 " pdb=" O12 PTY B 501 " ideal model delta sinusoidal sigma weight residual 300.23 134.78 165.45 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 2577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 412 0.023 - 0.047: 185 0.047 - 0.070: 80 0.070 - 0.094: 39 0.094 - 0.117: 22 Chirality restraints: 738 Sorted by residual: chirality pdb=" CA PRO B 180 " pdb=" N PRO B 180 " pdb=" C PRO B 180 " pdb=" CB PRO B 180 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA PRO A 180 " pdb=" N PRO A 180 " pdb=" C PRO A 180 " pdb=" CB PRO A 180 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.32e-01 chirality pdb=" CA ASN A 178 " pdb=" N ASN A 178 " pdb=" C ASN A 178 " pdb=" CB ASN A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.20e-01 ... (remaining 735 not shown) Planarity restraints: 764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 274 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C SER B 274 " -0.055 2.00e-02 2.50e+03 pdb=" O SER B 274 " 0.021 2.00e-02 2.50e+03 pdb=" N HIS B 275 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 274 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C SER A 274 " 0.055 2.00e-02 2.50e+03 pdb=" O SER A 274 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS A 275 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 272 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C VAL B 272 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL B 272 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL B 273 " -0.018 2.00e-02 2.50e+03 ... (remaining 761 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1084 2.80 - 3.32: 4614 3.32 - 3.85: 7333 3.85 - 4.37: 7859 4.37 - 4.90: 14047 Nonbonded interactions: 34937 Sorted by model distance: nonbonded pdb=" OD2 ASP B 208 " pdb=" OE2 GLU B 240 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP A 208 " pdb=" OE2 GLU A 240 " model vdw 2.272 3.040 nonbonded pdb=" CE1 HIS B 151 " pdb=" OE1 GLU B 276 " model vdw 2.282 3.260 nonbonded pdb=" CE1 HIS A 151 " pdb=" OE1 GLU A 276 " model vdw 2.282 3.260 nonbonded pdb=" OD1 ASP A 144 " pdb=" CE1 HIS A 149 " model vdw 2.285 3.260 ... (remaining 34932 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 6 through 309 or resid 402 through 403)) selection = (chain 'B' and (resid 6 through 309 or resid 502 through 503)) } 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=0.60 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: 0.180 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.660 Find NCS groups from input model: 0.090 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.004 0.069 4436 Z= 0.223 Angle : 0.871 16.520 6034 Z= 0.418 Chirality : 0.038 0.117 738 Planarity : 0.006 0.041 764 Dihedral : 15.230 165.450 1528 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.62 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.35), residues: 604 helix: 2.27 (0.24), residues: 482 sheet: None (None), residues: 0 loop : -3.12 (0.47), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.016 0.002 TYR B 145 PHE 0.010 0.002 PHE A 94 TRP 0.014 0.002 TRP B 168 HIS 0.006 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.22 ( 4436) covalent geometry : angle 0.87112 / 0.42 ( 6034) hydrogen bonds : bond 0.12833 / 9.17 ( 393) hydrogen bonds : angle 5.48685 / 4.12 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: B 89 ASP cc_start: 0.8787 (m-30) cc_final: 0.8524 (m-30) REVERT: B 157 GLN cc_start: 0.7995 (mm110) cc_final: 0.7716 (tt0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0741 time to fit residues: 10.3010 Evaluate side-chains 76 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.087349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.071114 restraints weight = 6890.659| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.43 r_work: 0.2932 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4436 Z= 0.154 Angle : 0.646 7.138 6034 Z= 0.319 Chirality : 0.036 0.115 738 Planarity : 0.005 0.039 764 Dihedral : 10.153 112.558 690 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.13 % Favored : 94.54 % Rotamer: Outliers : 2.18 % Allowed : 12.62 % Favored : 85.19 % 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 (0.36), residues: 604 helix: 2.87 (0.24), residues: 486 sheet: None (None), residues: 0 loop : -3.02 (0.51), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 195 TYR 0.012 0.001 TYR B 145 PHE 0.009 0.001 PHE A 94 TRP 0.006 0.001 TRP B 168 HIS 0.006 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 4436) covalent geometry : angle 0.64630 / 0.32 ( 6034) hydrogen bonds : bond 0.04703 / 3.22 ( 393) hydrogen bonds : angle 4.40126 / 3.28 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 145 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7203 (t80) REVERT: A 152 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8558 (tm-30) REVERT: A 160 GLU cc_start: 0.8464 (pp20) cc_final: 0.8233 (pp20) REVERT: A 193 ASP cc_start: 0.8447 (t0) cc_final: 0.7949 (t0) REVERT: B 67 PHE cc_start: 0.8709 (t80) cc_final: 0.8469 (t80) REVERT: B 75 LEU cc_start: 0.9453 (mm) cc_final: 0.9189 (mm) REVERT: B 89 ASP cc_start: 0.9070 (m-30) cc_final: 0.8620 (m-30) REVERT: B 157 GLN cc_start: 0.7864 (mm110) cc_final: 0.7614 (mm110) REVERT: B 170 PHE cc_start: 0.8706 (m-80) cc_final: 0.8506 (m-80) REVERT: B 262 MET cc_start: 0.9128 (mmm) cc_final: 0.8146 (mmm) REVERT: B 295 MET cc_start: 0.9323 (mmm) cc_final: 0.9005 (mmm) outliers start: 9 outliers final: 5 residues processed: 91 average time/residue: 0.0393 time to fit residues: 5.1423 Evaluate side-chains 81 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 298 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.088643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072077 restraints weight = 6077.684| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.25 r_work: 0.2953 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4436 Z= 0.139 Angle : 0.612 9.297 6034 Z= 0.299 Chirality : 0.035 0.119 738 Planarity : 0.004 0.041 764 Dihedral : 8.052 73.366 690 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.63 % Favored : 94.04 % Rotamer: Outliers : 1.70 % Allowed : 15.78 % Favored : 82.52 % 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: 3.10 (0.36), residues: 604 helix: 3.18 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -3.22 (0.48), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 195 TYR 0.007 0.001 TYR B 145 PHE 0.009 0.001 PHE A 94 TRP 0.005 0.001 TRP B 168 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 4436) covalent geometry : angle 0.61175 / 0.30 ( 6034) hydrogen bonds : bond 0.04546 / 3.12 ( 393) hydrogen bonds : angle 4.28357 / 3.21 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8723 (pp20) cc_final: 0.8488 (pp20) REVERT: A 193 ASP cc_start: 0.8435 (t0) cc_final: 0.7957 (t0) REVERT: B 67 PHE cc_start: 0.8731 (t80) cc_final: 0.8222 (t80) REVERT: B 75 LEU cc_start: 0.9493 (mm) cc_final: 0.9169 (mm) REVERT: B 89 ASP cc_start: 0.9021 (m-30) cc_final: 0.8553 (m-30) REVERT: B 157 GLN cc_start: 0.8125 (mm110) cc_final: 0.7873 (mm110) REVERT: B 170 PHE cc_start: 0.8732 (m-80) cc_final: 0.8473 (m-80) REVERT: B 295 MET cc_start: 0.9312 (mmm) cc_final: 0.9106 (mmm) outliers start: 7 outliers final: 7 residues processed: 93 average time/residue: 0.0425 time to fit residues: 5.6543 Evaluate side-chains 86 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 298 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.0060 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.089411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073033 restraints weight = 5979.144| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.22 r_work: 0.2970 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4436 Z= 0.129 Angle : 0.585 6.338 6034 Z= 0.287 Chirality : 0.035 0.121 738 Planarity : 0.004 0.043 764 Dihedral : 6.684 52.531 690 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.46 % Favored : 94.21 % Rotamer: Outliers : 1.46 % Allowed : 17.48 % Favored : 81.07 % 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: 3.23 (0.36), residues: 604 helix: 3.32 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -3.40 (0.47), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 195 TYR 0.005 0.001 TYR B 145 PHE 0.010 0.001 PHE A 94 TRP 0.005 0.001 TRP A 168 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 4436) covalent geometry : angle 0.58476 / 0.29 ( 6034) hydrogen bonds : bond 0.04172 / 2.87 ( 393) hydrogen bonds : angle 4.15809 / 3.12 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.157 Fit side-chains REVERT: A 67 PHE cc_start: 0.8895 (t80) cc_final: 0.8507 (t80) REVERT: A 160 GLU cc_start: 0.8731 (pp20) cc_final: 0.8416 (pp20) REVERT: A 193 ASP cc_start: 0.8515 (t0) cc_final: 0.8119 (t0) REVERT: B 67 PHE cc_start: 0.8741 (t80) cc_final: 0.8168 (t80) REVERT: B 89 ASP cc_start: 0.8987 (m-30) cc_final: 0.8496 (m-30) REVERT: B 157 GLN cc_start: 0.8133 (mm110) cc_final: 0.7913 (mm110) REVERT: B 170 PHE cc_start: 0.8767 (m-80) cc_final: 0.8544 (m-80) REVERT: B 262 MET cc_start: 0.9172 (mmm) cc_final: 0.8868 (mtp) REVERT: B 280 GLU cc_start: 0.8642 (mp0) cc_final: 0.8272 (mp0) REVERT: B 295 MET cc_start: 0.9324 (mmm) cc_final: 0.9085 (mmm) outliers start: 6 outliers final: 5 residues processed: 94 average time/residue: 0.0452 time to fit residues: 6.0781 Evaluate side-chains 90 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 238 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.072941 restraints weight = 5972.293| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.20 r_work: 0.2972 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4436 Z= 0.132 Angle : 0.589 6.235 6034 Z= 0.291 Chirality : 0.036 0.124 738 Planarity : 0.004 0.042 764 Dihedral : 6.125 50.218 690 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.30 % Favored : 94.37 % Rotamer: Outliers : 1.94 % Allowed : 19.66 % Favored : 78.40 % 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: 3.35 (0.36), residues: 604 helix: 3.41 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -3.40 (0.46), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 195 TYR 0.004 0.001 TYR B 145 PHE 0.009 0.001 PHE A 94 TRP 0.004 0.001 TRP A 168 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 4436) covalent geometry : angle 0.58871 / 0.29 ( 6034) hydrogen bonds : bond 0.04266 / 2.93 ( 393) hydrogen bonds : angle 4.13325 / 3.10 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.146 Fit side-chains REVERT: A 67 PHE cc_start: 0.8947 (t80) cc_final: 0.8487 (t80) REVERT: A 160 GLU cc_start: 0.8784 (pp20) cc_final: 0.8440 (pp20) REVERT: A 193 ASP cc_start: 0.8529 (t0) cc_final: 0.8140 (t0) REVERT: A 280 GLU cc_start: 0.8564 (mp0) cc_final: 0.8169 (mp0) REVERT: B 67 PHE cc_start: 0.8780 (t80) cc_final: 0.8274 (t80) REVERT: B 89 ASP cc_start: 0.9037 (m-30) cc_final: 0.8516 (m-30) REVERT: B 157 GLN cc_start: 0.8171 (mm110) cc_final: 0.7956 (mm110) REVERT: B 170 PHE cc_start: 0.8767 (m-80) cc_final: 0.8506 (m-80) REVERT: B 262 MET cc_start: 0.9264 (mmm) cc_final: 0.8925 (mtp) REVERT: B 280 GLU cc_start: 0.8612 (mp0) cc_final: 0.8333 (mp0) REVERT: B 295 MET cc_start: 0.9323 (mmm) cc_final: 0.9043 (mmm) REVERT: B 306 THR cc_start: 0.8284 (t) cc_final: 0.8016 (t) outliers start: 8 outliers final: 5 residues processed: 96 average time/residue: 0.0392 time to fit residues: 5.4145 Evaluate side-chains 92 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 238 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068219 restraints weight = 6296.895| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.27 r_work: 0.2864 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4436 Z= 0.165 Angle : 0.630 8.848 6034 Z= 0.313 Chirality : 0.036 0.121 738 Planarity : 0.004 0.041 764 Dihedral : 6.256 50.110 690 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.30 % Favored : 94.37 % Rotamer: Outliers : 1.94 % Allowed : 20.15 % Favored : 77.91 % 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: 3.28 (0.36), residues: 604 helix: 3.38 (0.23), residues: 482 sheet: None (None), residues: 0 loop : -3.39 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 283 TYR 0.005 0.001 TYR A 258 PHE 0.011 0.001 PHE A 94 TRP 0.005 0.001 TRP B 168 HIS 0.005 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 4436) covalent geometry : angle 0.63017 / 0.31 ( 6034) hydrogen bonds : bond 0.05199 / 3.57 ( 393) hydrogen bonds : angle 4.28576 / 3.22 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.160 Fit side-chains REVERT: A 160 GLU cc_start: 0.8878 (pp20) cc_final: 0.8565 (pp20) REVERT: A 193 ASP cc_start: 0.8497 (t0) cc_final: 0.8129 (t0) REVERT: A 280 GLU cc_start: 0.8585 (mp0) cc_final: 0.8170 (mp0) REVERT: A 306 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8726 (t) REVERT: B 67 PHE cc_start: 0.8941 (t80) cc_final: 0.8235 (t80) REVERT: B 89 ASP cc_start: 0.9185 (m-30) cc_final: 0.8611 (m-30) REVERT: B 157 GLN cc_start: 0.8172 (mm110) cc_final: 0.7901 (mm110) REVERT: B 170 PHE cc_start: 0.8794 (m-80) cc_final: 0.8511 (m-80) REVERT: B 207 GLN cc_start: 0.8342 (pp30) cc_final: 0.7999 (pp30) REVERT: B 280 GLU cc_start: 0.8643 (mp0) cc_final: 0.8328 (mp0) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.0414 time to fit residues: 5.3599 Evaluate side-chains 88 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 238 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.071248 restraints weight = 6171.863| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.25 r_work: 0.2922 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4436 Z= 0.137 Angle : 0.612 6.977 6034 Z= 0.303 Chirality : 0.036 0.133 738 Planarity : 0.004 0.042 764 Dihedral : 5.920 48.537 690 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.30 % Favored : 94.37 % Rotamer: Outliers : 2.18 % Allowed : 18.93 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.29 (0.36), residues: 604 helix: 3.36 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -3.37 (0.47), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 195 TYR 0.006 0.001 TYR B 145 PHE 0.010 0.001 PHE A 94 TRP 0.004 0.000 TRP B 168 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 4436) covalent geometry : angle 0.61170 / 0.30 ( 6034) hydrogen bonds : bond 0.04434 / 3.06 ( 393) hydrogen bonds : angle 4.19169 / 3.14 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.147 Fit side-chains REVERT: A 67 PHE cc_start: 0.8936 (t80) cc_final: 0.8393 (t80) REVERT: A 160 GLU cc_start: 0.8869 (pp20) cc_final: 0.8551 (pp20) REVERT: A 193 ASP cc_start: 0.8508 (t0) cc_final: 0.8150 (t0) REVERT: A 262 MET cc_start: 0.9371 (mmm) cc_final: 0.9016 (mtp) REVERT: A 280 GLU cc_start: 0.8561 (mp0) cc_final: 0.8164 (mp0) REVERT: A 306 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8549 (t) REVERT: B 67 PHE cc_start: 0.8865 (t80) cc_final: 0.8359 (t80) REVERT: B 89 ASP cc_start: 0.9138 (m-30) cc_final: 0.8591 (m-30) REVERT: B 157 GLN cc_start: 0.8149 (mm110) cc_final: 0.7918 (mm110) REVERT: B 170 PHE cc_start: 0.8792 (m-80) cc_final: 0.8491 (m-80) REVERT: B 207 GLN cc_start: 0.8610 (pp30) cc_final: 0.7970 (pp30) REVERT: B 262 MET cc_start: 0.9306 (mmm) cc_final: 0.8974 (mtp) REVERT: B 280 GLU cc_start: 0.8607 (mp0) cc_final: 0.8243 (mp0) REVERT: B 306 THR cc_start: 0.8302 (t) cc_final: 0.8024 (t) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 0.0395 time to fit residues: 5.2331 Evaluate side-chains 93 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 238 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.089683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.073087 restraints weight = 6060.953| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.22 r_work: 0.2979 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4436 Z= 0.131 Angle : 0.607 6.606 6034 Z= 0.300 Chirality : 0.036 0.141 738 Planarity : 0.004 0.042 764 Dihedral : 5.594 45.688 690 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.97 % Favored : 94.70 % Rotamer: Outliers : 2.18 % Allowed : 18.69 % Favored : 79.13 % 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: 3.27 (0.36), residues: 604 helix: 3.36 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -3.45 (0.46), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 195 TYR 0.004 0.001 TYR B 145 PHE 0.009 0.001 PHE A 94 TRP 0.003 0.000 TRP B 168 HIS 0.006 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 4436) covalent geometry : angle 0.60739 / 0.30 ( 6034) hydrogen bonds : bond 0.04193 / 2.88 ( 393) hydrogen bonds : angle 4.13577 / 3.10 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.150 Fit side-chains REVERT: A 67 PHE cc_start: 0.8945 (t80) cc_final: 0.8401 (t80) REVERT: A 160 GLU cc_start: 0.8907 (pp20) cc_final: 0.8585 (pp20) REVERT: A 193 ASP cc_start: 0.8549 (t0) cc_final: 0.8193 (t0) REVERT: A 280 GLU cc_start: 0.8540 (mp0) cc_final: 0.8148 (mp0) REVERT: A 306 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8474 (t) REVERT: B 38 LEU cc_start: 0.9456 (mm) cc_final: 0.9244 (tp) REVERT: B 67 PHE cc_start: 0.8845 (t80) cc_final: 0.8296 (t80) REVERT: B 89 ASP cc_start: 0.9075 (m-30) cc_final: 0.8534 (m-30) REVERT: B 170 PHE cc_start: 0.8781 (m-80) cc_final: 0.8473 (m-80) REVERT: B 207 GLN cc_start: 0.8352 (pp30) cc_final: 0.7672 (pp30) REVERT: B 262 MET cc_start: 0.9310 (mmm) cc_final: 0.9000 (mtp) REVERT: B 280 GLU cc_start: 0.8602 (mp0) cc_final: 0.8238 (mp0) REVERT: B 306 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7983 (t) outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.0400 time to fit residues: 5.6718 Evaluate side-chains 98 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 306 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.089959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.072954 restraints weight = 5582.439| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.10 r_work: 0.2996 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4436 Z= 0.130 Angle : 0.609 6.766 6034 Z= 0.302 Chirality : 0.036 0.149 738 Planarity : 0.004 0.041 764 Dihedral : 5.442 43.514 690 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.30 % Favored : 94.37 % Rotamer: Outliers : 3.16 % Allowed : 18.69 % Favored : 78.16 % 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: 3.21 (0.36), residues: 604 helix: 3.34 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -3.75 (0.43), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 195 TYR 0.004 0.001 TYR B 145 PHE 0.010 0.001 PHE A 94 TRP 0.003 0.000 TRP A 168 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 4436) covalent geometry : angle 0.60893 / 0.30 ( 6034) hydrogen bonds : bond 0.04149 / 2.85 ( 393) hydrogen bonds : angle 4.10590 / 3.07 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.151 Fit side-chains REVERT: A 67 PHE cc_start: 0.8942 (t80) cc_final: 0.8346 (t80) REVERT: A 160 GLU cc_start: 0.8939 (pp20) cc_final: 0.8615 (pp20) REVERT: A 193 ASP cc_start: 0.8547 (t0) cc_final: 0.8180 (t0) REVERT: A 262 MET cc_start: 0.9377 (mmm) cc_final: 0.9042 (mtp) REVERT: A 280 GLU cc_start: 0.8524 (mp0) cc_final: 0.8135 (mp0) REVERT: A 306 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8444 (t) REVERT: B 67 PHE cc_start: 0.8829 (t80) cc_final: 0.8267 (t80) REVERT: B 89 ASP cc_start: 0.9039 (m-30) cc_final: 0.8486 (m-30) REVERT: B 262 MET cc_start: 0.9311 (mmm) cc_final: 0.8997 (mtp) REVERT: B 280 GLU cc_start: 0.8614 (mp0) cc_final: 0.8227 (mp0) REVERT: B 306 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7934 (t) outliers start: 13 outliers final: 8 residues processed: 94 average time/residue: 0.0432 time to fit residues: 5.8498 Evaluate side-chains 95 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 306 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072285 restraints weight = 6026.396| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.20 r_work: 0.2958 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4436 Z= 0.140 Angle : 0.628 7.200 6034 Z= 0.313 Chirality : 0.036 0.156 738 Planarity : 0.004 0.040 764 Dihedral : 5.453 43.797 690 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.30 % Favored : 94.37 % Rotamer: Outliers : 2.43 % Allowed : 19.42 % Favored : 78.16 % 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: 3.26 (0.36), residues: 604 helix: 3.37 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -3.67 (0.44), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 283 TYR 0.004 0.001 TYR A 258 PHE 0.012 0.001 PHE B 94 TRP 0.004 0.000 TRP B 168 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 4436) covalent geometry : angle 0.62755 / 0.31 ( 6034) hydrogen bonds : bond 0.04469 / 3.06 ( 393) hydrogen bonds : angle 4.12152 / 3.10 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.154 Fit side-chains REVERT: A 67 PHE cc_start: 0.8953 (t80) cc_final: 0.8310 (t80) REVERT: A 160 GLU cc_start: 0.8975 (pp20) cc_final: 0.8665 (pp20) REVERT: A 193 ASP cc_start: 0.8581 (t0) cc_final: 0.8212 (t0) REVERT: A 280 GLU cc_start: 0.8527 (mp0) cc_final: 0.8136 (mp0) REVERT: A 306 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8522 (t) REVERT: B 67 PHE cc_start: 0.8832 (t80) cc_final: 0.8120 (t80) REVERT: B 89 ASP cc_start: 0.9103 (m-30) cc_final: 0.8549 (m-30) REVERT: B 207 GLN cc_start: 0.7780 (pp30) cc_final: 0.7163 (pp30) REVERT: B 262 MET cc_start: 0.9359 (mmm) cc_final: 0.9039 (mtp) REVERT: B 280 GLU cc_start: 0.8578 (mp0) cc_final: 0.8161 (mp0) REVERT: B 306 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7980 (t) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.0445 time to fit residues: 5.9505 Evaluate side-chains 93 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 306 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.069406 restraints weight = 6155.170| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.25 r_work: 0.2905 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4436 Z= 0.164 Angle : 0.667 9.091 6034 Z= 0.331 Chirality : 0.038 0.151 738 Planarity : 0.004 0.040 764 Dihedral : 5.768 46.035 690 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.79 % Favored : 93.87 % Rotamer: Outliers : 2.43 % Allowed : 20.15 % Favored : 77.43 % 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: 3.24 (0.36), residues: 604 helix: 3.33 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -3.56 (0.46), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 195 TYR 0.005 0.001 TYR B 258 PHE 0.013 0.001 PHE B 94 TRP 0.005 0.001 TRP B 168 HIS 0.005 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 4436) covalent geometry : angle 0.66686 / 0.33 ( 6034) hydrogen bonds : bond 0.05018 / 3.44 ( 393) hydrogen bonds : angle 4.26393 / 3.19 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 973.08 seconds wall clock time: 17 minutes 20.58 seconds (1040.58 seconds total)