Starting phenix.real_space_refine on Wed Jul 1 20:45:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8acc_15346/07_2026/8acc_15346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8acc_15346/07_2026/8acc_15346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8acc_15346/07_2026/8acc_15346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8acc_15346/07_2026/8acc_15346.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8acc_15346/07_2026/8acc_15346.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8acc_15346/07_2026/8acc_15346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8acc_15346/07_2026/8acc_15346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8acc_15346/07_2026/8acc_15346.map" } resolution = 2.9 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= 0.012 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 5 5.49 5 S 10 5.16 5 C 1104 2.51 5 N 309 2.21 5 O 351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1779 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1680 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 10, 'TRANS': 220} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.79, per 1000 atoms: 0.44 Number of scatterers: 1779 At special positions: 0 Unit cell: (85.2, 73.485, 123.54, 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 10 16.00 P 5 15.00 O 351 8.00 N 309 7.00 C 1104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 77.7 milliseconds 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 438 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 49.4% alpha, 4.8% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.518A pdb=" N ARG A 85 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.624A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 130 through 137 Processing helix chain 'A' and resid 137 through 149 removed outlier: 3.882A pdb=" N ALA A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.861A pdb=" N ASN A 157 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.544A pdb=" N VAL A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.531A pdb=" N ALA A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.992A pdb=" N GLU A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.502A pdb=" N ARG A 262 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 166 removed outlier: 4.034A pdb=" N GLU A 173 " --> pdb=" O ILE A 165 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.22 Time building geometry restraints manager: 0.26 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: 538 1.34 - 1.45: 271 1.45 - 1.57: 984 1.57 - 1.69: 9 1.69 - 1.80: 18 Bond restraints: 1820 Sorted by residual: bond pdb=" N PRO A 273 " pdb=" CA PRO A 273 " ideal model delta sigma weight residual 1.468 1.456 0.012 1.20e-02 6.94e+03 9.83e-01 bond pdb=" CA VAL A 286 " pdb=" CB VAL A 286 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.88e-01 bond pdb=" CA VAL A 289 " pdb=" CB VAL A 289 " ideal model delta sigma weight residual 1.536 1.526 0.010 1.17e-02 7.31e+03 7.02e-01 bond pdb=" CA VAL A 65 " pdb=" CB VAL A 65 " ideal model delta sigma weight residual 1.540 1.519 0.021 2.70e-02 1.37e+03 6.26e-01 bond pdb=" N GLY A 276 " pdb=" CA GLY A 276 " ideal model delta sigma weight residual 1.449 1.460 -0.011 1.45e-02 4.76e+03 5.73e-01 ... (remaining 1815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 2459 2.06 - 4.11: 37 4.11 - 6.17: 2 6.17 - 8.22: 5 8.22 - 10.28: 2 Bond angle restraints: 2505 Sorted by residual: angle pdb=" N PRO A 273 " pdb=" CA PRO A 273 " pdb=" CB PRO A 273 " ideal model delta sigma weight residual 103.27 110.20 -6.93 9.00e-01 1.23e+00 5.93e+01 angle pdb=" N PRO A 69 " pdb=" CA PRO A 69 " pdb=" CB PRO A 69 " ideal model delta sigma weight residual 103.08 110.52 -7.44 9.70e-01 1.06e+00 5.89e+01 angle pdb=" N PRO A 70 " pdb=" CA PRO A 70 " pdb=" CB PRO A 70 " ideal model delta sigma weight residual 103.25 110.45 -7.20 1.05e+00 9.07e-01 4.70e+01 angle pdb=" OP1 U B 6 " pdb=" P U B 6 " pdb=" OP2 U B 6 " ideal model delta sigma weight residual 119.60 109.32 10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" OP1 U B 4 " pdb=" P U B 4 " pdb=" OP2 U B 4 " ideal model delta sigma weight residual 119.60 109.53 10.07 3.00e+00 1.11e-01 1.13e+01 ... (remaining 2500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 974 15.33 - 30.66: 72 30.66 - 45.99: 21 45.99 - 61.32: 3 61.32 - 76.65: 1 Dihedral angle restraints: 1071 sinusoidal: 395 harmonic: 676 Sorted by residual: dihedral pdb=" N PRO A 70 " pdb=" C PRO A 70 " pdb=" CA PRO A 70 " pdb=" CB PRO A 70 " ideal model delta harmonic sigma weight residual 115.10 123.97 -8.87 0 2.50e+00 1.60e-01 1.26e+01 dihedral pdb=" N PRO A 69 " pdb=" C PRO A 69 " pdb=" CA PRO A 69 " pdb=" CB PRO A 69 " ideal model delta harmonic sigma weight residual 115.10 123.48 -8.38 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" CA TRP A 232 " pdb=" C TRP A 232 " pdb=" N LEU A 233 " pdb=" CA LEU A 233 " ideal model delta harmonic sigma weight residual -180.00 -165.06 -14.94 0 5.00e+00 4.00e-02 8.92e+00 ... (remaining 1068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 251 0.057 - 0.113: 41 0.113 - 0.170: 3 0.170 - 0.227: 1 0.227 - 0.283: 4 Chirality restraints: 300 Sorted by residual: chirality pdb=" CA PRO A 70 " pdb=" N PRO A 70 " pdb=" C PRO A 70 " pdb=" CB PRO A 70 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" P U B 6 " pdb=" OP1 U B 6 " pdb=" OP2 U B 6 " pdb=" O5' U B 6 " both_signs ideal model delta sigma weight residual True 2.41 -2.67 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO A 69 " pdb=" N PRO A 69 " pdb=" C PRO A 69 " pdb=" CB PRO A 69 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 297 not shown) Planarity restraints: 309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 256 " 0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" C ILE A 256 " -0.018 2.00e-02 2.50e+03 pdb=" O ILE A 256 " 0.007 2.00e-02 2.50e+03 pdb=" N ALA A 257 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 180 " 0.016 5.00e-02 4.00e+02 2.41e-02 9.33e-01 pdb=" N PRO A 181 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 159 " 0.004 2.00e-02 2.50e+03 7.32e-03 5.37e-01 pdb=" C HIS A 159 " -0.013 2.00e-02 2.50e+03 pdb=" O HIS A 159 " 0.005 2.00e-02 2.50e+03 pdb=" N THR A 160 " 0.004 2.00e-02 2.50e+03 ... (remaining 306 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 143 2.74 - 3.28: 1856 3.28 - 3.82: 2587 3.82 - 4.36: 3178 4.36 - 4.90: 5043 Nonbonded interactions: 12807 Sorted by model distance: nonbonded pdb=" O ALA A 258 " pdb=" OG1 THR A 261 " model vdw 2.200 3.040 nonbonded pdb=" O PRO A 181 " pdb=" ND2 ASN A 185 " model vdw 2.265 3.120 nonbonded pdb=" O VAL A 260 " pdb=" NH2 ARG A 263 " model vdw 2.273 3.120 nonbonded pdb=" O PRO A 188 " pdb=" OG1 THR A 189 " model vdw 2.307 3.040 nonbonded pdb=" OE2 GLU A 154 " pdb=" NZ LYS A 264 " model vdw 2.307 3.120 ... (remaining 12802 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.880 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.002 0.021 1820 Z= 0.126 Angle : 0.696 10.278 2505 Z= 0.420 Chirality : 0.051 0.283 300 Planarity : 0.002 0.024 309 Dihedral : 12.052 76.647 633 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 2.18 % Allowed : 11.35 % Favored : 86.46 % 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: -2.46 (0.55), residues: 229 helix: -1.18 (0.53), residues: 100 sheet: 1.20 (1.45), residues: 12 loop : -2.40 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 82 TYR 0.007 0.001 TYR A 205 PHE 0.007 0.001 PHE A 237 TRP 0.005 0.001 TRP A 161 HIS 0.001 0.000 HIS A 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 ( 1820) covalent geometry : angle 0.69611 / 0.42 ( 2505) hydrogen bonds : bond 0.25066 / 17.22 ( 64) hydrogen bonds : angle 6.96312 / 4.84 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.067 Fit side-chains REVERT: A 97 LYS cc_start: 0.8956 (mttp) cc_final: 0.7965 (tptt) REVERT: A 132 ASP cc_start: 0.7999 (t0) cc_final: 0.7764 (t0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.6225 time to fit residues: 36.0544 Evaluate side-chains 49 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.0020 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.0152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** 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 = 0.3611 r_free = 0.3611 target = 0.136383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120833 restraints weight = 2825.943| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.07 r_work: 0.3351 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1820 Z= 0.118 Angle : 0.562 5.520 2505 Z= 0.298 Chirality : 0.044 0.219 300 Planarity : 0.003 0.020 309 Dihedral : 6.542 38.125 304 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.92 % Favored : 88.65 % Rotamer: Outliers : 3.29 % Allowed : 15.79 % Favored : 80.92 % 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: -2.03 (0.55), residues: 229 helix: -0.77 (0.53), residues: 101 sheet: 1.17 (1.35), residues: 12 loop : -2.20 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.008 0.001 TYR A 92 PHE 0.008 0.001 PHE A 237 TRP 0.010 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 1820) covalent geometry : angle 0.56209 / 0.30 ( 2505) hydrogen bonds : bond 0.03469 / 2.48 ( 64) hydrogen bonds : angle 4.71834 / 3.21 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.070 Fit side-chains REVERT: A 92 TYR cc_start: 0.8930 (t80) cc_final: 0.8703 (t80) REVERT: A 97 LYS cc_start: 0.8927 (mttp) cc_final: 0.7891 (tptt) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.6272 time to fit residues: 35.6632 Evaluate side-chains 53 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** 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 = 0.3558 r_free = 0.3558 target = 0.132306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116415 restraints weight = 2857.368| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.11 r_work: 0.3295 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1820 Z= 0.153 Angle : 0.575 5.886 2505 Z= 0.304 Chirality : 0.046 0.259 300 Planarity : 0.003 0.019 309 Dihedral : 6.690 38.751 304 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.23 % Favored : 87.34 % Rotamer: Outliers : 4.61 % Allowed : 19.08 % Favored : 76.32 % 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 (0.55), residues: 229 helix: -0.61 (0.53), residues: 95 sheet: -0.56 (1.32), residues: 16 loop : -2.29 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.009 0.001 TYR A 92 PHE 0.010 0.002 PHE A 237 TRP 0.011 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 1820) covalent geometry : angle 0.57529 / 0.30 ( 2505) hydrogen bonds : bond 0.03301 / 2.36 ( 64) hydrogen bonds : angle 4.43578 / 3.05 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.084 Fit side-chains REVERT: A 92 TYR cc_start: 0.8970 (t80) cc_final: 0.8730 (t80) REVERT: A 97 LYS cc_start: 0.8914 (mttp) cc_final: 0.7873 (tptt) REVERT: A 194 MET cc_start: 0.9275 (mmm) cc_final: 0.9056 (mmp) REVERT: A 245 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8895 (p) REVERT: A 262 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7893 (ptp-110) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.5532 time to fit residues: 33.1566 Evaluate side-chains 58 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 264 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 20 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 0.0970 chunk 21 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN A 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115287 restraints weight = 2847.011| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.11 r_work: 0.3267 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1820 Z= 0.137 Angle : 0.558 5.880 2505 Z= 0.296 Chirality : 0.045 0.258 300 Planarity : 0.003 0.019 309 Dihedral : 6.767 39.636 304 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.92 % Favored : 88.65 % Rotamer: Outliers : 5.26 % Allowed : 21.05 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.55), residues: 229 helix: -0.37 (0.54), residues: 95 sheet: -0.73 (1.30), residues: 16 loop : -2.26 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.008 0.001 TYR A 92 PHE 0.008 0.001 PHE A 237 TRP 0.011 0.001 TRP A 161 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 1820) covalent geometry : angle 0.55842 / 0.30 ( 2505) hydrogen bonds : bond 0.02915 / 2.11 ( 64) hydrogen bonds : angle 4.32204 / 2.98 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.074 Fit side-chains REVERT: A 92 TYR cc_start: 0.8995 (t80) cc_final: 0.8752 (t80) REVERT: A 97 LYS cc_start: 0.8932 (mttp) cc_final: 0.7931 (tptt) REVERT: A 173 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: A 194 MET cc_start: 0.9232 (mmm) cc_final: 0.8997 (mmp) REVERT: A 247 LYS cc_start: 0.8641 (mmmm) cc_final: 0.8053 (mppt) REVERT: A 262 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7812 (ptp-110) outliers start: 8 outliers final: 3 residues processed: 56 average time/residue: 0.5667 time to fit residues: 32.2447 Evaluate side-chains 58 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 14 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** 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 = 0.3484 r_free = 0.3484 target = 0.127830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111949 restraints weight = 2882.473| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.10 r_work: 0.3219 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1820 Z= 0.195 Angle : 0.606 6.532 2505 Z= 0.320 Chirality : 0.048 0.304 300 Planarity : 0.004 0.018 309 Dihedral : 7.063 37.751 304 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.66 % Favored : 86.90 % Rotamer: Outliers : 5.92 % Allowed : 20.39 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.55), residues: 229 helix: -0.36 (0.54), residues: 95 sheet: -0.88 (1.30), residues: 16 loop : -2.29 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 239 TYR 0.012 0.002 TYR A 87 PHE 0.012 0.002 PHE A 237 TRP 0.012 0.001 TRP A 161 HIS 0.006 0.002 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 1820) covalent geometry : angle 0.60584 / 0.32 ( 2505) hydrogen bonds : bond 0.03294 / 2.35 ( 64) hydrogen bonds : angle 4.37968 / 3.05 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.053 Fit side-chains REVERT: A 92 TYR cc_start: 0.8996 (t80) cc_final: 0.8755 (t80) REVERT: A 97 LYS cc_start: 0.8927 (mttp) cc_final: 0.7906 (tptt) REVERT: A 173 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: A 243 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7518 (mp-120) REVERT: A 245 THR cc_start: 0.9254 (p) cc_final: 0.9024 (t) REVERT: A 247 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8117 (mppt) REVERT: A 262 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8099 (ptp-110) outliers start: 9 outliers final: 3 residues processed: 55 average time/residue: 0.5250 time to fit residues: 29.2882 Evaluate side-chains 58 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.0060 chunk 3 optimal weight: 5.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** 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 = 0.3549 r_free = 0.3549 target = 0.133062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117354 restraints weight = 2863.287| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.11 r_work: 0.3287 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1820 Z= 0.115 Angle : 0.541 5.388 2505 Z= 0.284 Chirality : 0.044 0.238 300 Planarity : 0.003 0.020 309 Dihedral : 6.771 40.888 304 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.92 % Favored : 88.21 % Rotamer: Outliers : 4.61 % Allowed : 24.34 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.56), residues: 229 helix: -0.04 (0.55), residues: 95 sheet: -0.83 (1.33), residues: 16 loop : -2.26 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 239 TYR 0.007 0.001 TYR A 205 PHE 0.006 0.001 PHE A 197 TRP 0.011 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 1820) covalent geometry : angle 0.54051 / 0.28 ( 2505) hydrogen bonds : bond 0.02642 / 1.92 ( 64) hydrogen bonds : angle 4.12604 / 2.86 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.074 Fit side-chains REVERT: A 92 TYR cc_start: 0.8979 (t80) cc_final: 0.8680 (t80) REVERT: A 97 LYS cc_start: 0.8859 (mttp) cc_final: 0.7853 (tptt) REVERT: A 247 LYS cc_start: 0.8683 (mmmm) cc_final: 0.7999 (mppt) REVERT: A 250 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: A 262 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7763 (ptp-110) outliers start: 7 outliers final: 5 residues processed: 58 average time/residue: 0.5055 time to fit residues: 29.8193 Evaluate side-chains 58 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 3 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115176 restraints weight = 2817.251| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.09 r_work: 0.3256 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1820 Z= 0.149 Angle : 0.567 5.724 2505 Z= 0.298 Chirality : 0.045 0.262 300 Planarity : 0.004 0.028 309 Dihedral : 6.831 39.342 304 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.87 % Allowed : 12.66 % Favored : 86.46 % Rotamer: Outliers : 4.61 % Allowed : 25.66 % Favored : 69.74 % 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 are not related in a simple way. whole: -1.79 (0.56), residues: 229 helix: -0.04 (0.54), residues: 95 sheet: -0.93 (1.34), residues: 16 loop : -2.27 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 82 TYR 0.012 0.001 TYR A 87 PHE 0.009 0.001 PHE A 237 TRP 0.012 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 1820) covalent geometry : angle 0.56740 / 0.30 ( 2505) hydrogen bonds : bond 0.02859 / 2.05 ( 64) hydrogen bonds : angle 4.16950 / 2.89 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.040 Fit side-chains REVERT: A 92 TYR cc_start: 0.8974 (t80) cc_final: 0.8726 (t80) REVERT: A 97 LYS cc_start: 0.8890 (mttp) cc_final: 0.7883 (tptt) REVERT: A 247 LYS cc_start: 0.8750 (mmmm) cc_final: 0.8058 (mppt) REVERT: A 250 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: A 256 ILE cc_start: 0.9219 (mm) cc_final: 0.8986 (mt) REVERT: A 262 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8041 (ptp-110) outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 0.4031 time to fit residues: 24.1551 Evaluate side-chains 62 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114155 restraints weight = 2856.194| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.09 r_work: 0.3241 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1820 Z= 0.171 Angle : 0.597 5.995 2505 Z= 0.314 Chirality : 0.046 0.280 300 Planarity : 0.003 0.022 309 Dihedral : 6.976 40.024 304 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.87 % Allowed : 11.35 % Favored : 87.77 % Rotamer: Outliers : 4.61 % Allowed : 26.97 % Favored : 68.42 % 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: -1.80 (0.56), residues: 229 helix: -0.05 (0.54), residues: 95 sheet: -1.03 (1.34), residues: 16 loop : -2.26 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.007 0.001 TYR A 205 PHE 0.010 0.001 PHE A 237 TRP 0.011 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 1820) covalent geometry : angle 0.59660 / 0.31 ( 2505) hydrogen bonds : bond 0.03004 / 2.15 ( 64) hydrogen bonds : angle 4.19695 / 2.92 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.040 Fit side-chains REVERT: A 92 TYR cc_start: 0.8987 (t80) cc_final: 0.8721 (t80) REVERT: A 97 LYS cc_start: 0.8903 (mttp) cc_final: 0.7888 (tptt) REVERT: A 247 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8065 (mppt) REVERT: A 250 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: A 262 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8130 (ptp-110) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.3537 time to fit residues: 20.4815 Evaluate side-chains 59 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 19 optimal weight: 0.0170 chunk 20 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117792 restraints weight = 2850.310| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.14 r_work: 0.3299 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1820 Z= 0.114 Angle : 0.550 5.010 2505 Z= 0.289 Chirality : 0.043 0.218 300 Planarity : 0.004 0.031 309 Dihedral : 6.762 41.442 304 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.48 % Favored : 88.65 % Rotamer: Outliers : 5.92 % Allowed : 27.63 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.56), residues: 229 helix: 0.21 (0.54), residues: 95 sheet: -1.08 (1.37), residues: 14 loop : -2.25 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 82 TYR 0.007 0.001 TYR A 92 PHE 0.006 0.001 PHE A 237 TRP 0.011 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 1820) covalent geometry : angle 0.55026 / 0.29 ( 2505) hydrogen bonds : bond 0.02497 / 1.81 ( 64) hydrogen bonds : angle 4.02477 / 2.79 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.037 Fit side-chains REVERT: A 92 TYR cc_start: 0.8974 (t80) cc_final: 0.8730 (t80) REVERT: A 95 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8600 (tmtt) REVERT: A 97 LYS cc_start: 0.8863 (mttp) cc_final: 0.7908 (tptt) REVERT: A 199 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8663 (mm-30) REVERT: A 247 LYS cc_start: 0.8669 (mmmm) cc_final: 0.7980 (mppt) REVERT: A 250 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7477 (pm20) REVERT: A 256 ILE cc_start: 0.9187 (mm) cc_final: 0.8947 (mt) outliers start: 9 outliers final: 7 residues processed: 58 average time/residue: 0.3112 time to fit residues: 18.3735 Evaluate side-chains 61 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 0.0370 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 19 optimal weight: 0.0970 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116788 restraints weight = 2827.705| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.09 r_work: 0.3282 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1820 Z= 0.127 Angle : 0.569 5.734 2505 Z= 0.299 Chirality : 0.044 0.224 300 Planarity : 0.003 0.032 309 Dihedral : 6.750 40.702 304 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.48 % Favored : 88.65 % Rotamer: Outliers : 6.58 % Allowed : 25.66 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.56), residues: 229 helix: 0.21 (0.54), residues: 95 sheet: -1.09 (1.39), residues: 14 loop : -2.21 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 82 TYR 0.012 0.001 TYR A 87 PHE 0.006 0.001 PHE A 237 TRP 0.012 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 1820) covalent geometry : angle 0.56922 / 0.30 ( 2505) hydrogen bonds : bond 0.02626 / 1.89 ( 64) hydrogen bonds : angle 4.04554 / 2.80 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.038 Fit side-chains REVERT: A 95 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8619 (tmtt) REVERT: A 97 LYS cc_start: 0.8918 (mttp) cc_final: 0.7904 (tptt) REVERT: A 247 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8029 (mppt) REVERT: A 250 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: A 256 ILE cc_start: 0.9234 (mm) cc_final: 0.8999 (mt) REVERT: A 262 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7878 (ptp-110) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.3618 time to fit residues: 21.3411 Evaluate side-chains 61 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 264 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 22 optimal weight: 30.0000 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118229 restraints weight = 2895.977| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.09 r_work: 0.3282 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1820 Z= 0.117 Angle : 0.574 5.013 2505 Z= 0.301 Chirality : 0.043 0.210 300 Planarity : 0.003 0.031 309 Dihedral : 6.670 41.106 304 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.48 % Favored : 88.65 % Rotamer: Outliers : 5.92 % Allowed : 27.63 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.57), residues: 229 helix: 0.37 (0.55), residues: 95 sheet: -1.10 (1.38), residues: 14 loop : -2.22 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 82 TYR 0.011 0.001 TYR A 87 PHE 0.006 0.001 PHE A 237 TRP 0.011 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 1820) covalent geometry : angle 0.57399 / 0.30 ( 2505) hydrogen bonds : bond 0.02455 / 1.77 ( 64) hydrogen bonds : angle 3.95570 / 2.74 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1046.33 seconds wall clock time: 18 minutes 27.87 seconds (1107.87 seconds total)