Starting phenix.real_space_refine on Thu Sep 10 23:06:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xlt_33286/09_2026/7xlt_33286.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xlt_33286/09_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_33286/09_2026/7xlt_33286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xlt_33286/09_2026/7xlt_33286.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xlt_33286/09_2026/7xlt_33286.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xlt_33286/09_2026/7xlt_33286.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xlt_33286/09_2026/7xlt_33286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xlt_33286/09_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-2.2.1-6174/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: {'RNAv2': 40} Modifications used: {'rna3p_pur': 32, 'rna3p_pyr': 8} Link IDs: {'rna3p': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 0.46 Conformation dependent library (CDL) restraints added in 93.7 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: 0.59 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: 0.62 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: 7071 2.07 - 4.14: 395 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: 2295 15.74 - 31.49: 399 31.49 - 47.23: 151 47.23 - 62.97: 39 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 - 0.133: 810 0.133 - 0.267: 61 0.267 - 0.400: 1 0.400 - 0.533: 0 0.533 - 0.667: 2 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 2.17 -2.84 -0.67 2.00e-01 2.50e+01 1.11e+01 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 2.17 -2.71 -0.54 2.00e-01 2.50e+01 7.29e+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 ... (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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.180 Find NCS groups from input model: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.950 ------------------------------------------------------------------------------- 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 : 0.006 0.052 5270 Z= 0.397 Angle : 0.993 10.357 7528 Z= 0.660 Chirality : 0.076 0.667 874 Planarity : 0.006 0.055 662 Dihedral : 17.373 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 0.00553 / 0.40 ( 5266) covalent geometry : angle 0.99206 / 0.66 ( 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 : 0.154 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: 0.0733 time to fit residues: 6.6750 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 : 0.211 ------------------------------------------------------------------------------- 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: 10.0000 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: 4.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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** L 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.147783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.118333 restraints weight = 33445.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.120594 restraints weight = 21124.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.121745 restraints weight = 15249.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.123060 restraints weight = 12355.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.123469 restraints weight = 10750.901| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5270 Z= 0.206 Angle : 0.779 6.586 7528 Z= 0.427 Chirality : 0.049 0.165 874 Planarity : 0.006 0.046 662 Dihedral : 13.233 61.282 1334 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: 0.17 (0.40), residues: 172 loop : -2.75 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 104 TYR 0.015 0.002 TYR H 27 PHE 0.023 0.003 PHE H 106 TRP 0.018 0.002 TRP H 47 HIS 0.017 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.21 ( 5266) covalent geometry : angle 0.77758 / 0.43 ( 7520) SS BOND : bond 0.00850 / 0.42 ( 4) SS BOND : angle 1.84052 / 0.81 ( 8) hydrogen bonds : bond 0.05490 / 3.52 ( 206) hydrogen bonds : angle 6.91827 / 4.42 ( 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 : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 109 TRP cc_start: 0.7544 (m-10) cc_final: 0.7313 (m-10) REVERT: L 60 PHE cc_start: 0.6317 (t80) cc_final: 0.6063 (t80) REVERT: L 78 LEU cc_start: 0.9014 (tt) cc_final: 0.8498 (tt) REVERT: L 129 GLN cc_start: 0.6324 (pt0) cc_final: 0.5930 (pm20) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0804 time to fit residues: 7.4542 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 : 0.102 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 48 optimal weight: 10.0000 chunk 32 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 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 = 0.4614 r_free = 0.4614 target = 0.149126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.120693 restraints weight = 32510.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.122689 restraints weight = 20899.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.123819 restraints weight = 15171.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.125098 restraints weight = 12304.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.125506 restraints weight = 10765.296| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5270 Z= 0.161 Angle : 0.710 6.995 7528 Z= 0.388 Chirality : 0.047 0.165 874 Planarity : 0.004 0.039 662 Dihedral : 12.775 58.868 1334 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.11 (0.39), residues: 427 helix: -3.89 (0.72), residues: 18 sheet: 0.03 (0.39), residues: 177 loop : -2.48 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 59 TYR 0.021 0.002 TYR L 92 PHE 0.017 0.002 PHE L 76 TRP 0.011 0.001 TRP L 40 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 ( 5266) covalent geometry : angle 0.70938 / 0.39 ( 7520) SS BOND : bond 0.00524 / 0.26 ( 4) SS BOND : angle 1.13805 / 0.51 ( 8) hydrogen bonds : bond 0.04678 / 2.91 ( 206) hydrogen bonds : angle 6.32218 / 4.04 ( 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 68 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: H 107 ASP cc_start: 0.5945 (p0) cc_final: 0.5677 (p0) REVERT: L 78 LEU cc_start: 0.9145 (tt) cc_final: 0.8781 (tt) REVERT: L 102 THR cc_start: 0.7916 (m) cc_final: 0.7706 (m) REVERT: L 171 GLN cc_start: 0.8119 (tp40) cc_final: 0.7702 (tp40) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0704 time to fit residues: 6.2962 Evaluate side-chains 55 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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: 8.9990 chunk 34 optimal weight: 20.0000 chunk 11 optimal weight: 0.0980 chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.0570 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 overall best weight: 2.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 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 = 0.4568 r_free = 0.4568 target = 0.145112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.115573 restraints weight = 33056.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.117753 restraints weight = 21060.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.118780 restraints weight = 15163.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.119616 restraints weight = 12198.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.120851 restraints weight = 10682.101| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2776 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= 0.187 Angle : 0.729 7.078 7528 Z= 0.393 Chirality : 0.047 0.158 874 Planarity : 0.005 0.051 662 Dihedral : 12.642 61.121 1334 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % 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: -2.15 (0.39), residues: 427 helix: -3.74 (0.79), residues: 18 sheet: -0.09 (0.38), residues: 177 loop : -2.42 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 59 TYR 0.012 0.002 TYR L 91 PHE 0.025 0.002 PHE L 76 TRP 0.016 0.002 TRP H 109 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 ( 5266) covalent geometry : angle 0.72780 / 0.39 ( 7520) SS BOND : bond 0.00558 / 0.28 ( 4) SS BOND : angle 1.26590 / 0.57 ( 8) hydrogen bonds : bond 0.05160 / 3.28 ( 206) hydrogen bonds : angle 6.32634 / 4.08 ( 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 61 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 107 ASP cc_start: 0.6598 (p0) cc_final: 0.6017 (p0) REVERT: L 4 MET cc_start: 0.8381 (tmm) cc_final: 0.8098 (tmm) REVERT: L 102 THR cc_start: 0.8080 (m) cc_final: 0.7782 (m) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0749 time to fit residues: 5.9966 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 : 0.108 ------------------------------------------------------------------------------- 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: 5.9990 chunk 14 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.4550 r_free = 0.4550 target = 0.143266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.118188 restraints weight = 34095.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.118115 restraints weight = 22535.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.118396 restraints weight = 16727.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.118574 restraints weight = 16173.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.118507 restraints weight = 13654.590| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5270 Z= 0.188 Angle : 0.737 9.209 7528 Z= 0.395 Chirality : 0.047 0.163 874 Planarity : 0.005 0.046 662 Dihedral : 12.522 63.386 1334 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.39), residues: 427 helix: -3.45 (0.86), residues: 18 sheet: 0.00 (0.39), residues: 170 loop : -2.39 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG L 24 TYR 0.015 0.002 TYR H 54 PHE 0.022 0.002 PHE L 76 TRP 0.030 0.003 TRP L 40 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.19 ( 5266) covalent geometry : angle 0.73636 / 0.40 ( 7520) SS BOND : bond 0.00653 / 0.32 ( 4) SS BOND : angle 1.23924 / 0.60 ( 8) hydrogen bonds : bond 0.05261 / 3.28 ( 206) hydrogen bonds : angle 6.28987 / 4.09 ( 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 58 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8337 (tmm) cc_final: 0.8095 (tmm) REVERT: L 92 TYR cc_start: 0.8221 (m-80) cc_final: 0.7493 (m-10) REVERT: L 171 GLN cc_start: 0.8216 (tp40) cc_final: 0.7795 (tp40) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0720 time to fit residues: 5.4874 Evaluate side-chains 47 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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: 7.9990 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 44 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.137890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.107367 restraints weight = 34123.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.109474 restraints weight = 21313.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.110900 restraints weight = 15391.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.111499 restraints weight = 12447.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.111688 restraints weight = 10943.409| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 5270 Z= 0.256 Angle : 0.849 9.445 7528 Z= 0.448 Chirality : 0.050 0.226 874 Planarity : 0.006 0.053 662 Dihedral : 12.596 64.687 1334 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 27.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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: -2.40 (0.39), residues: 427 helix: -4.18 (0.57), residues: 18 sheet: -0.32 (0.39), residues: 170 loop : -2.45 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.031 0.003 TYR L 191 PHE 0.027 0.003 PHE H 106 TRP 0.044 0.004 TRP L 40 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.26 ( 5266) covalent geometry : angle 0.84687 / 0.45 ( 7520) SS BOND : bond 0.00608 / 0.30 ( 4) SS BOND : angle 2.12303 / 1.09 ( 8) hydrogen bonds : bond 0.07106 / 4.64 ( 206) hydrogen bonds : angle 6.78634 / 4.43 ( 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 55 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: L 92 TYR cc_start: 0.8197 (m-80) cc_final: 0.7442 (m-10) REVERT: L 180 MET cc_start: 0.7110 (mmm) cc_final: 0.6331 (mmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0616 time to fit residues: 4.5313 Evaluate side-chains 44 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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: 6.9990 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 45 optimal weight: 50.0000 chunk 44 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 = 0.4497 r_free = 0.4497 target = 0.138935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.109579 restraints weight = 34275.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.111377 restraints weight = 22500.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.112306 restraints weight = 16695.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.113433 restraints weight = 13660.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.113559 restraints weight = 12061.001| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3768 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= 0.221 Angle : 0.807 8.678 7528 Z= 0.425 Chirality : 0.049 0.180 874 Planarity : 0.005 0.046 662 Dihedral : 12.581 65.378 1334 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % 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: -2.39 (0.40), residues: 427 helix: -4.17 (0.62), residues: 18 sheet: -0.23 (0.39), residues: 169 loop : -2.52 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 98 TYR 0.022 0.003 TYR L 191 PHE 0.013 0.002 PHE H 106 TRP 0.040 0.003 TRP L 40 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 ( 5266) covalent geometry : angle 0.80674 / 0.43 ( 7520) SS BOND : bond 0.00571 / 0.29 ( 4) SS BOND : angle 1.31466 / 0.65 ( 8) hydrogen bonds : bond 0.06378 / 4.06 ( 206) hydrogen bonds : angle 6.79207 / 4.40 ( 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 56 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: L 180 MET cc_start: 0.6467 (mmm) cc_final: 0.6239 (mmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0652 time to fit residues: 4.8871 Evaluate side-chains 45 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4505 r_free = 0.4505 target = 0.138993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.109344 restraints weight = 34126.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.111205 restraints weight = 22221.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.112503 restraints weight = 16268.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.112984 restraints weight = 13284.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.113708 restraints weight = 11757.891| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5270 Z= 0.191 Angle : 0.786 11.727 7528 Z= 0.414 Chirality : 0.049 0.192 874 Planarity : 0.005 0.043 662 Dihedral : 12.558 66.186 1334 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % 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: -2.25 (0.40), residues: 427 helix: -4.10 (0.65), residues: 18 sheet: -0.11 (0.40), residues: 169 loop : -2.44 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 98 TYR 0.025 0.002 TYR H 27 PHE 0.025 0.003 PHE L 103 TRP 0.043 0.004 TRP L 40 HIS 0.026 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 ( 5266) covalent geometry : angle 0.78481 / 0.41 ( 7520) SS BOND : bond 0.01240 / 0.62 ( 4) SS BOND : angle 1.75686 / 0.80 ( 8) hydrogen bonds : bond 0.05763 / 3.60 ( 206) hydrogen bonds : angle 6.73634 / 4.42 ( 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 55 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 92 TYR cc_start: 0.8155 (m-80) cc_final: 0.7754 (m-80) REVERT: L 180 MET cc_start: 0.6413 (mmm) cc_final: 0.6120 (tpt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0633 time to fit residues: 4.6428 Evaluate side-chains 44 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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: 2.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 0.0670 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- 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 = 0.4527 r_free = 0.4527 target = 0.140490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.111472 restraints weight = 33769.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.112938 restraints weight = 22120.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.114270 restraints weight = 16131.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.114804 restraints weight = 13134.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.115223 restraints weight = 11572.744| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 5270 Z= 0.180 Angle : 0.775 8.556 7528 Z= 0.409 Chirality : 0.049 0.183 874 Planarity : 0.005 0.043 662 Dihedral : 12.507 66.776 1334 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -2.14 (0.41), residues: 427 helix: -4.05 (0.68), residues: 18 sheet: 0.02 (0.41), residues: 169 loop : -2.40 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 98 TYR 0.025 0.002 TYR L 191 PHE 0.054 0.003 PHE L 76 TRP 0.045 0.004 TRP L 40 HIS 0.023 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 5266) covalent geometry : angle 0.77349 / 0.41 ( 7520) SS BOND : bond 0.00738 / 0.37 ( 4) SS BOND : angle 1.59543 / 0.70 ( 8) hydrogen bonds : bond 0.05383 / 3.33 ( 206) hydrogen bonds : angle 6.55293 / 4.30 ( 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 54 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: H 36 TRP cc_start: 0.7390 (m100) cc_final: 0.6676 (m100) REVERT: L 21 ILE cc_start: 0.8674 (mp) cc_final: 0.8465 (mp) REVERT: L 42 LEU cc_start: 0.8760 (tp) cc_final: 0.8554 (tp) REVERT: L 180 MET cc_start: 0.6224 (mmm) cc_final: 0.5925 (tpt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0704 time to fit residues: 5.0742 Evaluate side-chains 45 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 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 8 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 42 optimal weight: 50.0000 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 16 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.135524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.105194 restraints weight = 33965.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.107089 restraints weight = 21428.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.108437 restraints weight = 15484.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.109044 restraints weight = 12465.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.109228 restraints weight = 10953.070| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.005 0.060 5270 Z= 0.228 Angle : 0.825 10.353 7528 Z= 0.433 Chirality : 0.050 0.245 874 Planarity : 0.005 0.045 662 Dihedral : 12.573 66.572 1334 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 25.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % 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: -2.40 (0.40), residues: 427 helix: -4.12 (0.58), residues: 18 sheet: -0.37 (0.39), residues: 175 loop : -2.46 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 59 TYR 0.024 0.003 TYR L 191 PHE 0.020 0.003 PHE L 60 TRP 0.034 0.004 TRP L 40 HIS 0.021 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 ( 5266) covalent geometry : angle 0.82344 / 0.43 ( 7520) SS BOND : bond 0.00618 / 0.31 ( 4) SS BOND : angle 1.96590 / 0.90 ( 8) hydrogen bonds : bond 0.06514 / 4.19 ( 206) hydrogen bonds : angle 6.73660 / 4.44 ( 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 54 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8411 (tmm) cc_final: 0.8133 (tmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0644 time to fit residues: 4.6790 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 : 0.137 ------------------------------------------------------------------------------- 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: 8.9990 chunk 43 optimal weight: 30.0000 chunk 33 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4513 r_free = 0.4513 target = 0.140200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.114002 restraints weight = 34352.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.114106 restraints weight = 23244.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.114530 restraints weight = 17962.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.114876 restraints weight = 15395.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.114898 restraints weight = 14018.246| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5270 Z= 0.166 Angle : 0.768 9.677 7528 Z= 0.407 Chirality : 0.050 0.300 874 Planarity : 0.005 0.043 662 Dihedral : 12.473 66.979 1334 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % 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: -2.20 (0.40), residues: 427 helix: -4.06 (0.61), residues: 18 sheet: -0.02 (0.40), residues: 165 loop : -2.41 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 104 TYR 0.025 0.002 TYR L 191 PHE 0.016 0.002 PHE L 76 TRP 0.042 0.005 TRP L 40 HIS 0.018 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 ( 5266) covalent geometry : angle 0.76705 / 0.41 ( 7520) SS BOND : bond 0.00720 / 0.36 ( 4) SS BOND : angle 1.58002 / 0.73 ( 8) hydrogen bonds : bond 0.05227 / 3.21 ( 206) hydrogen bonds : angle 6.49870 / 4.29 ( 464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1138.71 seconds wall clock time: 20 minutes 21.97 seconds (1221.97 seconds total)