Starting phenix.real_space_refine on Thu Jul 2 01:08:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xlt_33286/07_2026/7xlt_33286.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xlt_33286/07_2026/7xlt_33286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xlt_33286/07_2026/7xlt_33286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xlt_33286/07_2026/7xlt_33286.map" model { file = "/net/cci-nas-00/data/ceres_data/7xlt_33286/07_2026/7xlt_33286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xlt_33286/07_2026/7xlt_33286.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xlt_33286/07_2026/7xlt_33286.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xlt_33286/07_2026/7xlt_33286.cif" } resolution = 4.4 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= -0.001 sd= 0.046 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 78 5.49 5 S 14 5.16 5 C 2869 2.51 5 N 845 2.21 5 O 1179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s 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: 4985 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1635 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 11, 'TRANS': 203} Chain: "L" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 11, 'TRANS': 204} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 801 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "B" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 873 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna3p_pur': 32, 'rna3p_pyr': 8} Link IDs: {'rna3p': 39} Time building chain proxies: 1.35, per 1000 atoms: 0.27 Number of scatterers: 4985 At special positions: 0 Unit cell: (125.465, 106.918, 93.826, 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 14 16.00 P 78 15.00 O 1179 8.00 N 845 7.00 C 2869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 201 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 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: 0.52 Conformation dependent library (CDL) restraints added in 145.5 milliseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 9 sheets defined 5.6% alpha, 36.0% beta 41 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.606A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 176 through 180 Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 188 through 192 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.340A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.340A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 129 removed outlier: 3.988A pdb=" N SER H 186 " --> pdb=" O HIS H 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 50 through 53 removed outlier: 5.817A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR L 107 " --> pdb=" O TYR L 91 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N CYS L 93 " --> pdb=" O GLY L 105 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY L 105 " --> pdb=" O CYS L 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 119 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 150 through 155 108 hydrogen bonds defined for protein. 264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1253 1.34 - 1.46: 1731 1.46 - 1.58: 2107 1.58 - 1.70: 156 1.70 - 1.82: 19 Bond restraints: 5266 Sorted by residual: bond pdb=" C1' DT A 35 " pdb=" N1 DT A 35 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" C1' DT A 9 " pdb=" N1 DT A 9 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.88e+00 bond pdb=" C1' DC A 27 " pdb=" N1 DC A 27 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 8.86e+00 bond pdb=" C1' DC A 19 " pdb=" N1 DC A 19 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.35e+00 bond pdb=" C1' DT A 21 " pdb=" N1 DT A 21 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.31e+00 ... (remaining 5261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 7148 2.07 - 4.14: 318 4.14 - 6.21: 41 6.21 - 8.29: 10 8.29 - 10.36: 3 Bond angle restraints: 7520 Sorted by residual: angle pdb=" C HIS L 98 " pdb=" N VAL L 99 " pdb=" CA VAL L 99 " ideal model delta sigma weight residual 120.24 123.82 -3.58 6.30e-01 2.52e+00 3.22e+01 angle pdb=" O4' DC A 17 " pdb=" C4' DC A 17 " pdb=" C3' DC A 17 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.25e+01 angle pdb=" O4' DC A 10 " pdb=" C4' DC A 10 " pdb=" C3' DC A 10 " ideal model delta sigma weight residual 106.00 103.27 2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" C PRO H 153 " pdb=" N GLU H 154 " pdb=" CA GLU H 154 " ideal model delta sigma weight residual 120.09 125.72 -5.63 1.25e+00 6.40e-01 2.03e+01 angle pdb=" O4' DT A 21 " pdb=" C4' DT A 21 " pdb=" C3' DT A 21 " ideal model delta sigma weight residual 106.00 103.32 2.68 6.00e-01 2.78e+00 2.00e+01 ... (remaining 7515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 2339 15.74 - 31.49: 395 31.49 - 47.23: 120 47.23 - 62.97: 30 62.97 - 78.72: 5 Dihedral angle restraints: 2889 sinusoidal: 1641 harmonic: 1248 Sorted by residual: dihedral pdb=" CA ASN L 58 " pdb=" C ASN L 58 " pdb=" N ARG L 59 " pdb=" CA ARG L 59 " ideal model delta harmonic sigma weight residual 180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA VAL H 156 " pdb=" C VAL H 156 " pdb=" N THR H 157 " pdb=" CA THR H 157 " ideal model delta harmonic sigma weight residual 180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA TYR H 80 " pdb=" C TYR H 80 " pdb=" N MET H 81 " pdb=" CA MET H 81 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 2886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 797 0.086 - 0.172: 69 0.172 - 0.258: 4 0.258 - 0.344: 3 0.344 - 0.430: 1 Chirality restraints: 874 Sorted by residual: chirality pdb=" P C B 37 " pdb=" OP1 C B 37 " pdb=" OP2 C B 37 " pdb=" O5' C B 37 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CB ILE L 155 " pdb=" CA ILE L 155 " pdb=" CG1 ILE L 155 " pdb=" CG2 ILE L 155 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" P C B 10 " pdb=" OP1 C B 10 " pdb=" OP2 C B 10 " pdb=" O5' C B 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 871 not shown) Planarity restraints: 662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 7 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO L 8 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 108 " 0.016 2.00e-02 2.50e+03 1.50e-02 4.50e+00 pdb=" CG TYR H 108 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR H 108 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR H 108 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR H 108 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 108 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 108 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 108 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 107 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" CG ASP H 107 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP H 107 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP H 107 " -0.012 2.00e-02 2.50e+03 ... (remaining 659 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1322 2.81 - 3.33: 3795 3.33 - 3.86: 9088 3.86 - 4.38: 9680 4.38 - 4.90: 15108 Nonbonded interactions: 38993 Sorted by model distance: nonbonded pdb=" O GLY H 8 " pdb=" OG1 THR H 113 " model vdw 2.288 3.040 nonbonded pdb=" OG SER H 141 " pdb=" O VAL H 189 " model vdw 2.326 3.040 nonbonded pdb=" OG SER L 57 " pdb=" O GLY L 69 " model vdw 2.337 3.040 nonbonded pdb=" OG SER L 25 " pdb=" O GLN L 27 " model vdw 2.353 3.040 nonbonded pdb=" NH1 ARG L 66 " pdb=" OE2 GLU L 84 " model vdw 2.369 3.120 ... (remaining 38988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.560 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 7.250 Find NCS groups from input model: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5270 Z= 0.398 Angle : 0.947 10.357 7528 Z= 0.654 Chirality : 0.054 0.430 874 Planarity : 0.006 0.055 662 Dihedral : 16.274 78.716 2081 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.79 % Allowed : 34.30 % Favored : 64.91 % 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: -2.19 (0.39), residues: 427 helix: -3.85 (0.81), residues: 12 sheet: 0.01 (0.39), residues: 188 loop : -2.75 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 66 TYR 0.037 0.002 TYR H 108 PHE 0.024 0.002 PHE L 94 TRP 0.024 0.003 TRP L 168 HIS 0.012 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.40 ( 5266) covalent geometry : angle 0.94668 / 0.65 ( 7520) SS BOND : bond 0.00513 / 0.25 ( 4) SS BOND : angle 1.39737 / 0.67 ( 8) hydrogen bonds : bond 0.10362 / 7.00 ( 206) hydrogen bonds : angle 7.41819 / 4.80 ( 464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 107 THR cc_start: 0.6878 (m) cc_final: 0.6515 (m) REVERT: L 171 GLN cc_start: 0.6884 (tp40) cc_final: 0.6116 (tp-100) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.0765 time to fit residues: 7.0133 Evaluate side-chains 62 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.147992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.118633 restraints weight = 33439.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.120807 restraints weight = 21088.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.121993 restraints weight = 15281.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.123353 restraints weight = 12339.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.123751 restraints weight = 10656.515| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5270 Z= 0.209 Angle : 0.732 6.279 7528 Z= 0.420 Chirality : 0.043 0.166 874 Planarity : 0.005 0.046 662 Dihedral : 11.207 57.781 1334 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: -2.27 (0.39), residues: 427 helix: -4.02 (0.64), residues: 18 sheet: 0.15 (0.40), residues: 172 loop : -2.74 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 104 TYR 0.014 0.002 TYR H 27 PHE 0.025 0.003 PHE H 106 TRP 0.016 0.003 TRP H 47 HIS 0.014 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.21 ( 5266) covalent geometry : angle 0.73010 / 0.42 ( 7520) SS BOND : bond 0.00839 / 0.42 ( 4) SS BOND : angle 1.90741 / 0.85 ( 8) hydrogen bonds : bond 0.05455 / 3.49 ( 206) hydrogen bonds : angle 6.87533 / 4.39 ( 464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 109 TRP cc_start: 0.7532 (m-10) cc_final: 0.7301 (m-10) REVERT: L 60 PHE cc_start: 0.6250 (t80) cc_final: 0.5975 (t80) REVERT: L 78 LEU cc_start: 0.9042 (tt) cc_final: 0.8535 (tt) REVERT: L 129 GLN cc_start: 0.6280 (pt0) cc_final: 0.5879 (pm20) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0759 time to fit residues: 7.2594 Evaluate side-chains 51 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.144621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.116837 restraints weight = 34475.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.118112 restraints weight = 25128.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.119136 restraints weight = 18202.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.119152 restraints weight = 14521.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.119295 restraints weight = 14478.199| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5270 Z= 0.198 Angle : 0.705 8.202 7528 Z= 0.400 Chirality : 0.043 0.174 874 Planarity : 0.005 0.040 662 Dihedral : 10.977 56.150 1334 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.26 % Allowed : 3.69 % Favored : 96.04 % 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: -2.26 (0.39), residues: 427 helix: -3.81 (0.72), residues: 18 sheet: -0.16 (0.38), residues: 177 loop : -2.50 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 24 TYR 0.019 0.002 TYR L 92 PHE 0.025 0.002 PHE L 76 TRP 0.021 0.002 TRP L 40 HIS 0.008 0.002 HIS H 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.20 ( 5266) covalent geometry : angle 0.70409 / 0.40 ( 7520) SS BOND : bond 0.01065 / 0.53 ( 4) SS BOND : angle 1.29744 / 0.61 ( 8) hydrogen bonds : bond 0.05419 / 3.40 ( 206) hydrogen bonds : angle 6.41232 / 4.13 ( 464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 102 THR cc_start: 0.8091 (m) cc_final: 0.7829 (m) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.0737 time to fit residues: 6.2547 Evaluate side-chains 49 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.0970 chunk 34 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 23 optimal weight: 0.4980 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.144867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.119774 restraints weight = 34287.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.119676 restraints weight = 22485.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.119750 restraints weight = 17662.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.120000 restraints weight = 16579.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.120048 restraints weight = 14895.901| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5270 Z= 0.168 Angle : 0.678 6.958 7528 Z= 0.383 Chirality : 0.042 0.156 874 Planarity : 0.005 0.040 662 Dihedral : 10.958 59.249 1334 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: -2.21 (0.38), residues: 427 helix: -3.77 (0.77), residues: 18 sheet: -0.02 (0.38), residues: 170 loop : -2.50 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 59 TYR 0.014 0.002 TYR H 54 PHE 0.020 0.002 PHE L 76 TRP 0.014 0.002 TRP L 40 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 ( 5266) covalent geometry : angle 0.67764 / 0.38 ( 7520) SS BOND : bond 0.00475 / 0.24 ( 4) SS BOND : angle 1.17063 / 0.53 ( 8) hydrogen bonds : bond 0.04960 / 3.06 ( 206) hydrogen bonds : angle 6.40109 / 4.15 ( 464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 60 PHE cc_start: 0.5761 (t80) cc_final: 0.5520 (t80) REVERT: L 92 TYR cc_start: 0.8143 (m-10) cc_final: 0.7566 (m-80) REVERT: L 94 PHE cc_start: 0.7129 (t80) cc_final: 0.6877 (t80) REVERT: L 102 THR cc_start: 0.7998 (m) cc_final: 0.7711 (m) REVERT: L 129 GLN cc_start: 0.6589 (pt0) cc_final: 0.5791 (pm20) REVERT: L 171 GLN cc_start: 0.8240 (tp40) cc_final: 0.7954 (tp40) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0696 time to fit residues: 5.7862 Evaluate side-chains 48 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 205 HIS ** 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 = 0.4568 r_free = 0.4568 target = 0.145071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.115171 restraints weight = 33857.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.117510 restraints weight = 21271.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.118589 restraints weight = 15184.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.119088 restraints weight = 12314.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.120486 restraints weight = 10950.523| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5270 Z= 0.154 Angle : 0.660 6.919 7528 Z= 0.371 Chirality : 0.042 0.158 874 Planarity : 0.004 0.038 662 Dihedral : 10.912 57.257 1334 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.39), residues: 427 helix: -3.50 (0.90), residues: 18 sheet: 0.03 (0.39), residues: 170 loop : -2.40 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 59 TYR 0.015 0.001 TYR H 94 PHE 0.019 0.002 PHE L 76 TRP 0.027 0.003 TRP H 36 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 ( 5266) covalent geometry : angle 0.65982 / 0.37 ( 7520) SS BOND : bond 0.00588 / 0.30 ( 4) SS BOND : angle 1.05164 / 0.49 ( 8) hydrogen bonds : bond 0.04740 / 2.90 ( 206) hydrogen bonds : angle 6.31727 / 4.12 ( 464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 60 PHE cc_start: 0.5524 (t80) cc_final: 0.5276 (t80) REVERT: L 92 TYR cc_start: 0.8226 (m-10) cc_final: 0.7490 (m-80) REVERT: L 107 THR cc_start: 0.8178 (m) cc_final: 0.7906 (m) REVERT: L 171 GLN cc_start: 0.8362 (tp40) cc_final: 0.8089 (tp-100) REVERT: L 180 MET cc_start: 0.6891 (mmm) cc_final: 0.5975 (mmm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0778 time to fit residues: 6.4395 Evaluate side-chains 50 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.0370 chunk 29 optimal weight: 20.0000 chunk 44 optimal weight: 40.0000 chunk 49 optimal weight: 30.0000 chunk 5 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 0.0570 chunk 47 optimal weight: 9.9990 overall best weight: 1.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 205 HIS ** 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 = 0.4586 r_free = 0.4586 target = 0.146411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.117376 restraints weight = 35022.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.119339 restraints weight = 22104.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.120804 restraints weight = 15996.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 73)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.121893 restraints weight = 12845.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.122497 restraints weight = 11095.212| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5270 Z= 0.150 Angle : 0.661 6.813 7528 Z= 0.368 Chirality : 0.042 0.227 874 Planarity : 0.005 0.042 662 Dihedral : 10.849 55.965 1334 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: -2.04 (0.39), residues: 427 helix: -3.41 (0.86), residues: 18 sheet: 0.02 (0.39), residues: 169 loop : -2.33 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.017 0.002 TYR L 191 PHE 0.019 0.002 PHE L 76 TRP 0.025 0.002 TRP L 40 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 ( 5266) covalent geometry : angle 0.66044 / 0.37 ( 7520) SS BOND : bond 0.00562 / 0.28 ( 4) SS BOND : angle 0.92999 / 0.42 ( 8) hydrogen bonds : bond 0.04554 / 2.77 ( 206) hydrogen bonds : angle 6.17105 / 4.03 ( 464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 MET cc_start: 0.7858 (tpp) cc_final: 0.7493 (tpt) REVERT: H 107 ASP cc_start: 0.6604 (p0) cc_final: 0.5867 (p0) REVERT: L 21 ILE cc_start: 0.8478 (mp) cc_final: 0.8269 (mp) REVERT: L 60 PHE cc_start: 0.5597 (t80) cc_final: 0.5240 (t80) REVERT: L 92 TYR cc_start: 0.8234 (m-10) cc_final: 0.7473 (m-80) REVERT: L 107 THR cc_start: 0.8062 (m) cc_final: 0.7822 (m) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0814 time to fit residues: 6.8552 Evaluate side-chains 51 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 29 optimal weight: 0.0670 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 45 optimal weight: 50.0000 chunk 44 optimal weight: 40.0000 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 GLN ** 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 = 0.4607 r_free = 0.4607 target = 0.148959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.120301 restraints weight = 34728.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.122167 restraints weight = 22465.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.123800 restraints weight = 16346.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.124781 restraints weight = 13102.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.124950 restraints weight = 11376.256| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5270 Z= 0.145 Angle : 0.652 6.674 7528 Z= 0.363 Chirality : 0.042 0.219 874 Planarity : 0.004 0.037 662 Dihedral : 10.762 55.874 1334 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: -2.06 (0.39), residues: 427 helix: -3.69 (0.73), residues: 18 sheet: 0.06 (0.40), residues: 169 loop : -2.37 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG L 82 TYR 0.010 0.001 TYR L 197 PHE 0.018 0.002 PHE L 94 TRP 0.029 0.002 TRP L 40 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 ( 5266) covalent geometry : angle 0.65158 / 0.36 ( 7520) SS BOND : bond 0.00602 / 0.30 ( 4) SS BOND : angle 0.92426 / 0.42 ( 8) hydrogen bonds : bond 0.04359 / 2.67 ( 206) hydrogen bonds : angle 6.00335 / 3.90 ( 464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 20 MET cc_start: 0.7846 (tpp) cc_final: 0.6974 (tpt) REVERT: H 107 ASP cc_start: 0.7097 (p0) cc_final: 0.5439 (p0) REVERT: L 21 ILE cc_start: 0.8487 (mp) cc_final: 0.8280 (mp) REVERT: L 60 PHE cc_start: 0.5515 (t80) cc_final: 0.5115 (t80) REVERT: L 171 GLN cc_start: 0.8207 (tp40) cc_final: 0.7805 (tp40) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0814 time to fit residues: 6.8297 Evaluate side-chains 49 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 0.0020 chunk 35 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** 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 = 0.4551 r_free = 0.4551 target = 0.143228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.114404 restraints weight = 33860.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.116235 restraints weight = 22268.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.117138 restraints weight = 16331.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.118214 restraints weight = 13371.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.118502 restraints weight = 11740.123| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5270 Z= 0.177 Angle : 0.668 6.916 7528 Z= 0.374 Chirality : 0.042 0.199 874 Planarity : 0.005 0.047 662 Dihedral : 10.821 56.474 1334 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.10 (0.40), residues: 427 helix: -3.62 (0.77), residues: 18 sheet: -0.09 (0.39), residues: 177 loop : -2.36 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 66 TYR 0.028 0.002 TYR H 27 PHE 0.021 0.002 PHE L 76 TRP 0.038 0.004 TRP L 40 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 ( 5266) covalent geometry : angle 0.66769 / 0.37 ( 7520) SS BOND : bond 0.00599 / 0.30 ( 4) SS BOND : angle 1.17465 / 0.56 ( 8) hydrogen bonds : bond 0.05145 / 3.26 ( 206) hydrogen bonds : angle 6.07714 / 3.94 ( 464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 MET cc_start: 0.8018 (tpp) cc_final: 0.7377 (tpt) REVERT: H 107 ASP cc_start: 0.7211 (p0) cc_final: 0.5370 (p0) REVERT: L 21 ILE cc_start: 0.8613 (mp) cc_final: 0.8343 (mp) REVERT: L 42 LEU cc_start: 0.8740 (tp) cc_final: 0.8395 (tp) REVERT: L 60 PHE cc_start: 0.5544 (t80) cc_final: 0.5237 (t80) REVERT: L 79 LYS cc_start: 0.8030 (tppt) cc_final: 0.7798 (tppt) REVERT: L 92 TYR cc_start: 0.8284 (m-10) cc_final: 0.7502 (m-10) REVERT: L 107 THR cc_start: 0.8395 (m) cc_final: 0.8192 (m) REVERT: L 171 GLN cc_start: 0.8282 (tp40) cc_final: 0.7965 (tp40) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0710 time to fit residues: 5.6783 Evaluate side-chains 50 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 ASN ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.136701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.107299 restraints weight = 34431.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.108522 restraints weight = 23387.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.109446 restraints weight = 17286.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.109668 restraints weight = 14121.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.110840 restraints weight = 12963.129| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 5270 Z= 0.260 Angle : 0.789 8.204 7528 Z= 0.432 Chirality : 0.045 0.178 874 Planarity : 0.006 0.052 662 Dihedral : 11.193 59.218 1334 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 27.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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 (0.39), residues: 427 helix: -3.47 (0.90), residues: 18 sheet: -0.32 (0.39), residues: 177 loop : -2.61 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG L 24 TYR 0.023 0.002 TYR H 27 PHE 0.022 0.003 PHE H 106 TRP 0.043 0.004 TRP L 40 HIS 0.010 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.26 ( 5266) covalent geometry : angle 0.78594 / 0.43 ( 7520) SS BOND : bond 0.00998 / 0.50 ( 4) SS BOND : angle 2.24511 / 1.02 ( 8) hydrogen bonds : bond 0.07218 / 4.73 ( 206) hydrogen bonds : angle 6.71350 / 4.40 ( 464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 20 MET cc_start: 0.8028 (tpp) cc_final: 0.7596 (tpt) REVERT: H 107 ASP cc_start: 0.7179 (p0) cc_final: 0.5108 (p0) REVERT: L 24 ARG cc_start: 0.7570 (tmt170) cc_final: 0.7370 (tmt170) REVERT: L 42 LEU cc_start: 0.8672 (tp) cc_final: 0.8396 (tp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0754 time to fit residues: 5.5002 Evaluate side-chains 51 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 50.0000 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 49 optimal weight: 30.0000 chunk 23 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** 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 = 0.4497 r_free = 0.4497 target = 0.138367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.108305 restraints weight = 34459.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.110025 restraints weight = 23040.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.111276 restraints weight = 17205.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.111869 restraints weight = 14105.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.111995 restraints weight = 12423.512| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5270 Z= 0.205 Angle : 0.735 7.257 7528 Z= 0.407 Chirality : 0.044 0.191 874 Planarity : 0.005 0.044 662 Dihedral : 11.260 58.715 1334 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.45 (0.39), residues: 427 helix: -3.41 (0.89), residues: 18 sheet: -0.20 (0.39), residues: 169 loop : -2.69 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 98 TYR 0.037 0.003 TYR L 191 PHE 0.016 0.002 PHE L 76 TRP 0.041 0.004 TRP H 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 ( 5266) covalent geometry : angle 0.73316 / 0.41 ( 7520) SS BOND : bond 0.00747 / 0.37 ( 4) SS BOND : angle 1.75443 / 0.79 ( 8) hydrogen bonds : bond 0.06204 / 3.94 ( 206) hydrogen bonds : angle 6.58718 / 4.32 ( 464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: H 20 MET cc_start: 0.7856 (tpp) cc_final: 0.7253 (tpt) REVERT: H 107 ASP cc_start: 0.7250 (p0) cc_final: 0.5158 (p0) REVERT: L 92 TYR cc_start: 0.8354 (m-10) cc_final: 0.7856 (m-80) REVERT: L 107 THR cc_start: 0.8486 (m) cc_final: 0.8269 (m) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0806 time to fit residues: 6.2023 Evaluate side-chains 50 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 0.0770 chunk 43 optimal weight: 30.0000 chunk 33 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** 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 = 0.4530 r_free = 0.4530 target = 0.141857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.111675 restraints weight = 34536.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.113807 restraints weight = 21635.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.114845 restraints weight = 15496.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.116198 restraints weight = 12452.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.116578 restraints weight = 10864.420| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5270 Z= 0.161 Angle : 0.719 9.546 7528 Z= 0.396 Chirality : 0.043 0.191 874 Planarity : 0.005 0.041 662 Dihedral : 11.252 58.086 1334 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -2.26 (0.40), residues: 427 helix: -3.36 (0.91), residues: 18 sheet: -0.09 (0.40), residues: 169 loop : -2.53 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.017 0.002 TYR H 27 PHE 0.024 0.002 PHE L 103 TRP 0.037 0.004 TRP H 109 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 ( 5266) covalent geometry : angle 0.71782 / 0.40 ( 7520) SS BOND : bond 0.00792 / 0.40 ( 4) SS BOND : angle 1.60707 / 0.71 ( 8) hydrogen bonds : bond 0.05255 / 3.24 ( 206) hydrogen bonds : angle 6.27121 / 4.13 ( 464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1220.14 seconds wall clock time: 21 minutes 42.48 seconds (1302.48 seconds total)