Starting phenix.real_space_refine on Fri Aug 22 14:25:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yry_39553/08_2025/8yry_39553.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yry_39553/08_2025/8yry_39553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yry_39553/08_2025/8yry_39553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yry_39553/08_2025/8yry_39553.map" model { file = "/net/cci-nas-00/data/ceres_data/8yry_39553/08_2025/8yry_39553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yry_39553/08_2025/8yry_39553.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2551 2.51 5 N 688 2.21 5 O 811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4068 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain breaks: 3 Chain: "H" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1665 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 13, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Time building chain proxies: 1.38, per 1000 atoms: 0.34 Number of scatterers: 4068 At special positions: 0 Unit cell: (111.188, 62.092, 69.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 811 8.00 N 688 7.00 C 2551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.24 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 164 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.03 Simple disulfide: pdb=" SG CYS L 153 " - pdb=" SG CYS L 213 " distance=2.01 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: 0.32 Conformation dependent library (CDL) restraints added in 163.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 6.4% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.001A pdb=" N CYS A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 182 No H-bonds generated for 'chain 'H' and resid 180 through 182' Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'L' and resid 98 through 102 removed outlier: 4.257A pdb=" N ILE L 102 " --> pdb=" O PRO L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 147 removed outlier: 3.659A pdb=" N LEU L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS L 145 " --> pdb=" O ASP L 141 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 206 removed outlier: 3.758A pdb=" N GLU L 206 " --> pdb=" O LYS L 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 202 through 206' Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'H' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.665A pdb=" N VAL H 31 " --> pdb=" O THR H 134 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TRP H 54 " --> pdb=" O TYR H 70 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR H 70 " --> pdb=" O TRP H 54 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP H 56 " --> pdb=" O MET H 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.191A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.191A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 174 through 178 removed outlier: 4.678A pdb=" N TYR H 218 " --> pdb=" O VAL H 235 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR H 229 " --> pdb=" O HIS H 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 30 through 32 removed outlier: 5.782A pdb=" N LEU L 30 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP L 54 " --> pdb=" O LEU L 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 38 through 42 Processing sheet with id=AA9, first strand: chain 'L' and resid 133 through 137 removed outlier: 5.796A pdb=" N TYR L 192 " --> pdb=" O ASN L 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 163 through 169 128 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 711 1.32 - 1.45: 1124 1.45 - 1.57: 2304 1.57 - 1.69: 0 1.69 - 1.82: 21 Bond restraints: 4160 Sorted by residual: bond pdb=" N PRO L 160 " pdb=" CD PRO L 160 " ideal model delta sigma weight residual 1.473 1.518 -0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" CA LEU A 77 " pdb=" C LEU A 77 " ideal model delta sigma weight residual 1.525 1.560 -0.035 1.11e-02 8.12e+03 1.01e+01 bond pdb=" C PRO H 143 " pdb=" O PRO H 143 " ideal model delta sigma weight residual 1.234 1.202 0.032 1.08e-02 8.57e+03 8.60e+00 bond pdb=" N VAL L 34 " pdb=" CA VAL L 34 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.85e+00 bond pdb=" N VAL H 208 " pdb=" CA VAL H 208 " ideal model delta sigma weight residual 1.462 1.486 -0.024 8.70e-03 1.32e+04 7.56e+00 ... (remaining 4155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 5403 2.51 - 5.01: 199 5.01 - 7.52: 44 7.52 - 10.03: 9 10.03 - 12.53: 1 Bond angle restraints: 5656 Sorted by residual: angle pdb=" N GLN A 78 " pdb=" CA GLN A 78 " pdb=" C GLN A 78 " ideal model delta sigma weight residual 112.89 103.65 9.24 1.24e+00 6.50e-01 5.56e+01 angle pdb=" N LEU L 144 " pdb=" CA LEU L 144 " pdb=" C LEU L 144 " ideal model delta sigma weight residual 111.36 103.43 7.93 1.09e+00 8.42e-01 5.30e+01 angle pdb=" N SER H 50 " pdb=" CA SER H 50 " pdb=" C SER H 50 " ideal model delta sigma weight residual 111.55 102.72 8.83 1.37e+00 5.33e-01 4.15e+01 angle pdb=" N SER L 71 " pdb=" CA SER L 71 " pdb=" C SER L 71 " ideal model delta sigma weight residual 110.80 123.33 -12.53 2.13e+00 2.20e-01 3.46e+01 angle pdb=" C PRO L 160 " pdb=" CA PRO L 160 " pdb=" CB PRO L 160 " ideal model delta sigma weight residual 111.71 119.21 -7.50 1.30e+00 5.92e-01 3.33e+01 ... (remaining 5651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 2167 17.36 - 34.72: 247 34.72 - 52.08: 67 52.08 - 69.44: 12 69.44 - 86.80: 9 Dihedral angle restraints: 2502 sinusoidal: 973 harmonic: 1529 Sorted by residual: dihedral pdb=" CB CYS L 42 " pdb=" SG CYS L 42 " pdb=" SG CYS L 107 " pdb=" CB CYS L 107 " ideal model delta sinusoidal sigma weight residual 93.00 166.03 -73.03 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS A 190 " pdb=" SG CYS A 190 " pdb=" SG CYS A 202 " pdb=" CB CYS A 202 " ideal model delta sinusoidal sigma weight residual -86.00 -158.59 72.59 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS L 153 " pdb=" SG CYS L 153 " pdb=" SG CYS L 213 " pdb=" CB CYS L 213 " ideal model delta sinusoidal sigma weight residual -86.00 -133.83 47.83 1 1.00e+01 1.00e-02 3.16e+01 ... (remaining 2499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 505 0.072 - 0.144: 105 0.144 - 0.216: 15 0.216 - 0.288: 9 0.288 - 0.360: 3 Chirality restraints: 637 Sorted by residual: chirality pdb=" CA SER L 71 " pdb=" N SER L 71 " pdb=" C SER L 71 " pdb=" CB SER L 71 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA TYR L 159 " pdb=" N TYR L 159 " pdb=" C TYR L 159 " pdb=" CB TYR L 159 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA SER L 26 " pdb=" N SER L 26 " pdb=" C SER L 26 " pdb=" CB SER L 26 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 634 not shown) Planarity restraints: 724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO L 27 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C PRO L 27 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO L 27 " -0.017 2.00e-02 2.50e+03 pdb=" N SER L 28 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU L 113 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO L 114 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO L 114 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 114 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 159 " -0.027 2.00e-02 2.50e+03 1.43e-02 4.09e+00 pdb=" CG TYR L 159 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR L 159 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR L 159 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR L 159 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR L 159 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR L 159 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR L 159 " -0.010 2.00e-02 2.50e+03 ... (remaining 721 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 549 2.75 - 3.29: 3862 3.29 - 3.83: 6646 3.83 - 4.36: 7991 4.36 - 4.90: 13722 Nonbonded interactions: 32770 Sorted by model distance: nonbonded pdb=" O ALA L 44 " pdb=" OG SER L 45 " model vdw 2.216 3.040 nonbonded pdb=" O ASP H 122 " pdb=" OD1 ASP H 122 " model vdw 2.221 3.040 nonbonded pdb=" O ILE L 125 " pdb=" OH TYR L 159 " model vdw 2.238 3.040 nonbonded pdb=" O ARG A 132 " pdb=" OH TYR H 121 " model vdw 2.252 3.040 nonbonded pdb=" O TYR H 73 " pdb=" NH1 ARG H 91 " model vdw 2.253 3.120 ... (remaining 32765 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.050 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:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 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 0.212 4167 Z= 0.341 Angle : 1.109 12.533 5670 Z= 0.692 Chirality : 0.068 0.360 637 Planarity : 0.005 0.057 724 Dihedral : 16.466 86.803 1499 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.15 % Allowed : 24.68 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.36), residues: 518 helix: -5.62 (0.35), residues: 7 sheet: 0.14 (0.37), residues: 184 loop : -2.17 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 76 TYR 0.027 0.002 TYR L 159 PHE 0.020 0.002 PHE L 158 TRP 0.019 0.002 TRP H 127 HIS 0.004 0.001 HIS H 188 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 4160) covalent geometry : angle 1.10807 ( 5656) SS BOND : bond 0.08073 ( 7) SS BOND : angle 1.41779 ( 14) hydrogen bonds : bond 0.15911 ( 113) hydrogen bonds : angle 8.71559 ( 336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: H 131 THR cc_start: 0.5655 (p) cc_final: 0.5165 (t) REVERT: H 238 LYS cc_start: 0.4852 (mttm) cc_final: 0.4222 (ptpp) outliers start: 10 outliers final: 5 residues processed: 58 average time/residue: 0.4560 time to fit residues: 27.5446 Evaluate side-chains 51 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN L 109 GLN ** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.212067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.186439 restraints weight = 4662.915| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.01 r_work: 0.4166 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4047 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4167 Z= 0.153 Angle : 0.667 6.630 5670 Z= 0.341 Chirality : 0.046 0.188 637 Planarity : 0.005 0.039 724 Dihedral : 6.460 49.464 573 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.94 % Allowed : 23.82 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.37), residues: 518 helix: -5.67 (0.31), residues: 7 sheet: 0.20 (0.37), residues: 196 loop : -1.94 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 91 TYR 0.015 0.002 TYR L 90 PHE 0.012 0.002 PHE H 124 TRP 0.011 0.002 TRP H 178 HIS 0.004 0.001 HIS H 188 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4160) covalent geometry : angle 0.66651 ( 5656) SS BOND : bond 0.00285 ( 7) SS BOND : angle 0.78322 ( 14) hydrogen bonds : bond 0.03186 ( 113) hydrogen bonds : angle 6.47288 ( 336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.6100 (mt) REVERT: A 195 TRP cc_start: 0.7049 (m100) cc_final: 0.6716 (m100) REVERT: H 24 GLN cc_start: 0.6326 (tp-100) cc_final: 0.6067 (tp-100) REVERT: H 131 THR cc_start: 0.5714 (p) cc_final: 0.5250 (t) REVERT: H 219 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6408 (pp) REVERT: H 238 LYS cc_start: 0.5037 (mttm) cc_final: 0.3885 (mtmm) REVERT: L 109 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7136 (pt0) outliers start: 23 outliers final: 8 residues processed: 67 average time/residue: 0.4155 time to fit residues: 29.0491 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 98 GLN Chi-restraints excluded: chain L residue 109 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 GLN ** L 217 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 = 0.4439 r_free = 0.4439 target = 0.213101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.187721 restraints weight = 4598.043| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 1.96 r_work: 0.4176 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4059 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4167 Z= 0.136 Angle : 0.641 6.590 5670 Z= 0.326 Chirality : 0.045 0.190 637 Planarity : 0.004 0.036 724 Dihedral : 5.920 47.799 568 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 4.51 % Allowed : 25.11 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.37), residues: 518 helix: -5.66 (0.30), residues: 7 sheet: 0.43 (0.38), residues: 191 loop : -1.94 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 91 TYR 0.013 0.002 TYR L 90 PHE 0.010 0.001 PHE A 76 TRP 0.026 0.002 TRP H 127 HIS 0.004 0.001 HIS H 188 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4160) covalent geometry : angle 0.64077 ( 5656) SS BOND : bond 0.00230 ( 7) SS BOND : angle 0.64556 ( 14) hydrogen bonds : bond 0.03000 ( 113) hydrogen bonds : angle 6.10464 ( 336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.161 Fit side-chains REVERT: H 24 GLN cc_start: 0.6420 (tp-100) cc_final: 0.6211 (tp40) REVERT: H 131 THR cc_start: 0.5767 (p) cc_final: 0.5389 (t) REVERT: H 219 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6781 (pp) REVERT: H 238 LYS cc_start: 0.5147 (mttm) cc_final: 0.3952 (mtmm) REVERT: L 109 GLN cc_start: 0.8090 (pp30) cc_final: 0.7213 (pt0) REVERT: L 145 LYS cc_start: 0.7315 (mmtp) cc_final: 0.7047 (mptt) outliers start: 21 outliers final: 12 residues processed: 66 average time/residue: 0.3742 time to fit residues: 25.9785 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 98 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 5 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN ** L 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 217 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 = 0.4472 r_free = 0.4472 target = 0.216595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.191387 restraints weight = 4521.394| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 1.95 r_work: 0.4177 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4061 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4167 Z= 0.110 Angle : 0.596 6.303 5670 Z= 0.303 Chirality : 0.044 0.175 637 Planarity : 0.004 0.038 724 Dihedral : 5.590 48.116 568 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.72 % Allowed : 25.75 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.37), residues: 518 helix: -5.66 (0.30), residues: 7 sheet: 0.56 (0.38), residues: 191 loop : -1.84 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 76 TYR 0.011 0.001 TYR L 159 PHE 0.008 0.001 PHE A 76 TRP 0.024 0.002 TRP H 127 HIS 0.002 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4160) covalent geometry : angle 0.59614 ( 5656) SS BOND : bond 0.00235 ( 7) SS BOND : angle 0.51682 ( 14) hydrogen bonds : bond 0.02723 ( 113) hydrogen bonds : angle 5.66578 ( 336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.153 Fit side-chains REVERT: A 195 TRP cc_start: 0.7009 (m100) cc_final: 0.6596 (m100) REVERT: H 131 THR cc_start: 0.5536 (p) cc_final: 0.5159 (t) REVERT: H 219 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6791 (pp) REVERT: H 238 LYS cc_start: 0.5217 (mttm) cc_final: 0.4000 (mtmm) REVERT: L 109 GLN cc_start: 0.8074 (pp30) cc_final: 0.7125 (pt0) REVERT: L 145 LYS cc_start: 0.7304 (mmtp) cc_final: 0.7065 (mptt) outliers start: 22 outliers final: 8 residues processed: 65 average time/residue: 0.3886 time to fit residues: 26.3757 Evaluate side-chains 52 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 98 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 GLN ** L 217 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 = 0.4379 r_free = 0.4379 target = 0.206177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.180854 restraints weight = 4648.877| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 1.95 r_work: 0.4106 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3989 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4167 Z= 0.194 Angle : 0.689 7.873 5670 Z= 0.353 Chirality : 0.047 0.178 637 Planarity : 0.005 0.038 724 Dihedral : 6.435 58.694 568 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.36 % Allowed : 26.18 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.37), residues: 518 helix: -5.64 (0.32), residues: 7 sheet: 0.46 (0.38), residues: 191 loop : -1.93 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 91 TYR 0.015 0.002 TYR L 90 PHE 0.014 0.002 PHE L 158 TRP 0.017 0.002 TRP H 127 HIS 0.004 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 4160) covalent geometry : angle 0.68865 ( 5656) SS BOND : bond 0.00312 ( 7) SS BOND : angle 0.79959 ( 14) hydrogen bonds : bond 0.03328 ( 113) hydrogen bonds : angle 6.32164 ( 336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.109 Fit side-chains REVERT: H 57 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7238 (mt) REVERT: H 238 LYS cc_start: 0.5190 (mttm) cc_final: 0.3826 (mtmm) REVERT: L 109 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7764 (pt0) outliers start: 25 outliers final: 14 residues processed: 64 average time/residue: 0.3214 time to fit residues: 21.6665 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 98 GLN Chi-restraints excluded: chain L residue 109 GLN Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN H 55 ASN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.209819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.184539 restraints weight = 4686.487| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.00 r_work: 0.4136 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4022 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4167 Z= 0.139 Angle : 0.632 7.047 5670 Z= 0.322 Chirality : 0.045 0.183 637 Planarity : 0.004 0.046 724 Dihedral : 5.962 53.369 568 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.29 % Allowed : 27.90 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.37), residues: 518 helix: -5.64 (0.32), residues: 7 sheet: 0.45 (0.38), residues: 191 loop : -1.84 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 91 TYR 0.012 0.002 TYR L 90 PHE 0.010 0.001 PHE H 124 TRP 0.022 0.002 TRP H 127 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4160) covalent geometry : angle 0.63225 ( 5656) SS BOND : bond 0.00215 ( 7) SS BOND : angle 0.59633 ( 14) hydrogen bonds : bond 0.02990 ( 113) hydrogen bonds : angle 5.90071 ( 336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.175 Fit side-chains REVERT: H 131 THR cc_start: 0.5681 (p) cc_final: 0.5438 (t) REVERT: H 219 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6758 (mm) REVERT: H 238 LYS cc_start: 0.5187 (mttm) cc_final: 0.3867 (mtmm) outliers start: 20 outliers final: 11 residues processed: 57 average time/residue: 0.4325 time to fit residues: 25.8109 Evaluate side-chains 50 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 98 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN ** L 217 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 = 0.4415 r_free = 0.4415 target = 0.210962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.185736 restraints weight = 4697.066| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.01 r_work: 0.4148 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4035 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4167 Z= 0.131 Angle : 0.618 6.950 5670 Z= 0.315 Chirality : 0.045 0.148 637 Planarity : 0.004 0.048 724 Dihedral : 5.557 31.918 568 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.08 % Allowed : 28.54 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.37), residues: 518 helix: -5.63 (0.33), residues: 7 sheet: 0.42 (0.38), residues: 192 loop : -1.75 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 91 TYR 0.011 0.002 TYR L 159 PHE 0.009 0.001 PHE A 76 TRP 0.022 0.002 TRP H 127 HIS 0.002 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4160) covalent geometry : angle 0.61842 ( 5656) SS BOND : bond 0.00211 ( 7) SS BOND : angle 0.55699 ( 14) hydrogen bonds : bond 0.02920 ( 113) hydrogen bonds : angle 5.73460 ( 336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.158 Fit side-chains REVERT: H 238 LYS cc_start: 0.5171 (mttm) cc_final: 0.3884 (mtmm) outliers start: 19 outliers final: 12 residues processed: 54 average time/residue: 0.4059 time to fit residues: 22.9361 Evaluate side-chains 50 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 98 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 0.0370 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.0030 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 overall best weight: 0.3068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 59 GLN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN L 108 GLN ** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.218376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.193320 restraints weight = 4564.183| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.02 r_work: 0.4183 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4167 Z= 0.111 Angle : 0.594 6.836 5670 Z= 0.301 Chirality : 0.044 0.124 637 Planarity : 0.004 0.048 724 Dihedral : 5.038 27.561 566 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.22 % Allowed : 28.97 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.37), residues: 518 helix: -5.63 (0.33), residues: 7 sheet: 0.43 (0.38), residues: 192 loop : -1.65 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 91 TYR 0.010 0.001 TYR L 159 PHE 0.008 0.001 PHE A 76 TRP 0.020 0.002 TRP H 127 HIS 0.001 0.001 HIS H 224 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 4160) covalent geometry : angle 0.59360 ( 5656) SS BOND : bond 0.00172 ( 7) SS BOND : angle 0.60857 ( 14) hydrogen bonds : bond 0.02735 ( 113) hydrogen bonds : angle 5.43333 ( 336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.158 Fit side-chains REVERT: H 24 GLN cc_start: 0.6224 (tp-100) cc_final: 0.6014 (tp40) REVERT: H 63 LYS cc_start: 0.6860 (tppp) cc_final: 0.6558 (ttmt) REVERT: H 238 LYS cc_start: 0.5193 (mttm) cc_final: 0.3920 (mtmm) outliers start: 15 outliers final: 11 residues processed: 60 average time/residue: 0.4455 time to fit residues: 27.9915 Evaluate side-chains 56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 98 GLN Chi-restraints excluded: chain L residue 174 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 0.0870 chunk 51 optimal weight: 0.0980 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 40 optimal weight: 0.0470 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 22 GLN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN L 108 GLN L 174 GLN ** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.216221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.191673 restraints weight = 4632.295| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 1.94 r_work: 0.4209 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4091 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4167 Z= 0.108 Angle : 0.610 11.856 5670 Z= 0.301 Chirality : 0.044 0.142 637 Planarity : 0.004 0.049 724 Dihedral : 4.798 17.878 565 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.22 % Allowed : 30.26 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.37), residues: 518 helix: -5.62 (0.34), residues: 7 sheet: 0.45 (0.38), residues: 192 loop : -1.60 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 91 TYR 0.011 0.001 TYR H 53 PHE 0.008 0.001 PHE H 124 TRP 0.017 0.001 TRP H 127 HIS 0.001 0.000 HIS H 224 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4160) covalent geometry : angle 0.61054 ( 5656) SS BOND : bond 0.00146 ( 7) SS BOND : angle 0.57497 ( 14) hydrogen bonds : bond 0.02643 ( 113) hydrogen bonds : angle 5.29803 ( 336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.171 Fit side-chains REVERT: H 24 GLN cc_start: 0.6360 (tp-100) cc_final: 0.6149 (tp40) REVERT: H 63 LYS cc_start: 0.6917 (tppp) cc_final: 0.6615 (ttmt) REVERT: H 238 LYS cc_start: 0.5196 (mttm) cc_final: 0.3957 (mtmm) REVERT: L 180 GLU cc_start: 0.6184 (mp0) cc_final: 0.5813 (tt0) outliers start: 15 outliers final: 12 residues processed: 57 average time/residue: 0.4182 time to fit residues: 24.9753 Evaluate side-chains 56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 98 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN L 46 GLN L 109 GLN ** L 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.213271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.188022 restraints weight = 4587.261| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 1.96 r_work: 0.4169 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4055 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4167 Z= 0.128 Angle : 0.634 11.360 5670 Z= 0.315 Chirality : 0.044 0.128 637 Planarity : 0.004 0.046 724 Dihedral : 4.921 18.308 565 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.89 % Rotamer: Outliers : 3.22 % Allowed : 30.04 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.37), residues: 518 helix: -5.62 (0.35), residues: 7 sheet: 0.44 (0.38), residues: 192 loop : -1.59 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 91 TYR 0.013 0.002 TYR H 53 PHE 0.009 0.001 PHE H 124 TRP 0.018 0.002 TRP H 127 HIS 0.002 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4160) covalent geometry : angle 0.63395 ( 5656) SS BOND : bond 0.00178 ( 7) SS BOND : angle 0.55069 ( 14) hydrogen bonds : bond 0.02730 ( 113) hydrogen bonds : angle 5.44645 ( 336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.101 Fit side-chains REVERT: H 63 LYS cc_start: 0.6896 (tppp) cc_final: 0.6578 (ttmt) REVERT: H 238 LYS cc_start: 0.5189 (mttm) cc_final: 0.3948 (mtmm) outliers start: 15 outliers final: 13 residues processed: 56 average time/residue: 0.4132 time to fit residues: 24.2057 Evaluate side-chains 56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 98 GLN Chi-restraints excluded: chain L residue 109 GLN Chi-restraints excluded: chain L residue 202 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.0000 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 GLN ** L 217 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 = 0.4432 r_free = 0.4432 target = 0.212157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.187012 restraints weight = 4601.020| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 1.95 r_work: 0.4161 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4046 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4167 Z= 0.133 Angle : 0.640 11.295 5670 Z= 0.319 Chirality : 0.044 0.124 637 Planarity : 0.004 0.043 724 Dihedral : 5.007 18.844 565 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.11 % Favored : 91.70 % Rotamer: Outliers : 3.00 % Allowed : 30.47 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.37), residues: 518 helix: -5.61 (0.35), residues: 7 sheet: 0.39 (0.38), residues: 192 loop : -1.59 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 91 TYR 0.012 0.002 TYR H 53 PHE 0.009 0.002 PHE H 124 TRP 0.018 0.002 TRP H 127 HIS 0.002 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4160) covalent geometry : angle 0.64046 ( 5656) SS BOND : bond 0.00173 ( 7) SS BOND : angle 0.55205 ( 14) hydrogen bonds : bond 0.02768 ( 113) hydrogen bonds : angle 5.47342 ( 336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.92 seconds wall clock time: 30 minutes 24.91 seconds (1824.91 seconds total)