Starting phenix.real_space_refine on Fri Aug 22 17:02:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sks_40566/08_2025/8sks_40566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sks_40566/08_2025/8sks_40566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sks_40566/08_2025/8sks_40566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sks_40566/08_2025/8sks_40566.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sks_40566/08_2025/8sks_40566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sks_40566/08_2025/8sks_40566.map" } resolution = 2.91 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= 0.019 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 Mn 4 7.51 5 S 16 5.16 5 C 3992 2.51 5 N 1092 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s 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: 6232 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1557 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 187} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 0.99, per 1000 atoms: 0.16 Number of scatterers: 6232 At special positions: 0 Unit cell: (71.69, 86.67, 86.67, 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) Mn 4 24.99 S 16 16.00 O 1128 8.00 N 1092 7.00 C 3992 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: 0.39 Conformation dependent library (CDL) restraints added in 265.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 69.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 34 through 39 removed outlier: 4.275A pdb=" N LEU A 38 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 76 removed outlier: 3.915A pdb=" N HIS A 55 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 105 Proline residue: A 86 - end of helix removed outlier: 3.627A pdb=" N THR A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.517A pdb=" N TYR A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 222 Processing helix chain 'B' and resid 34 through 39 removed outlier: 4.276A pdb=" N LEU B 38 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 76 removed outlier: 3.914A pdb=" N HIS B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 105 Proline residue: B 86 - end of helix removed outlier: 3.628A pdb=" N THR B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 196 through 205 removed outlier: 3.516A pdb=" N TYR B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 222 Processing helix chain 'C' and resid 34 through 39 removed outlier: 4.276A pdb=" N LEU C 38 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 39 " --> pdb=" O GLY C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 76 removed outlier: 3.915A pdb=" N HIS C 55 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 105 Proline residue: C 86 - end of helix removed outlier: 3.627A pdb=" N THR C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.517A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 222 Processing helix chain 'D' and resid 34 through 39 removed outlier: 4.275A pdb=" N LEU D 38 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU D 39 " --> pdb=" O GLY D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 76 removed outlier: 3.915A pdb=" N HIS D 55 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 105 Proline residue: D 86 - end of helix removed outlier: 3.628A pdb=" N THR D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 Processing helix chain 'D' and resid 127 through 142 Processing helix chain 'D' and resid 169 through 174 Processing helix chain 'D' and resid 185 through 188 Processing helix chain 'D' and resid 189 through 194 Processing helix chain 'D' and resid 196 through 205 removed outlier: 3.517A pdb=" N TYR D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 165 removed outlier: 7.322A pdb=" N GLY A 146 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP A 183 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY A 148 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY A 181 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 150 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 165 removed outlier: 7.323A pdb=" N GLY B 146 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP B 183 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 148 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY B 181 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 150 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 158 through 165 removed outlier: 7.323A pdb=" N GLY C 146 " --> pdb=" O ASP C 183 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP C 183 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY C 148 " --> pdb=" O GLY C 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 181 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 150 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 158 through 165 removed outlier: 7.322A pdb=" N GLY D 146 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP D 183 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY D 148 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY D 181 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 150 " --> pdb=" O LEU D 179 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1164 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: 0.62 Time building geometry restraints manager: 0.50 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: 2041 1.34 - 1.46: 1253 1.46 - 1.57: 3094 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 6412 Sorted by residual: bond pdb=" CA LYS D 221 " pdb=" C LYS D 221 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.28e-02 6.10e+03 1.61e+00 bond pdb=" CA VAL A 196 " pdb=" CB VAL A 196 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.31e-02 5.83e+03 1.45e+00 bond pdb=" CA LYS C 221 " pdb=" C LYS C 221 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.28e-02 6.10e+03 1.45e+00 bond pdb=" CA LYS B 221 " pdb=" C LYS B 221 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.28e-02 6.10e+03 1.45e+00 bond pdb=" CA VAL B 196 " pdb=" CB VAL B 196 " ideal model delta sigma weight residual 1.527 1.542 -0.016 1.31e-02 5.83e+03 1.41e+00 ... (remaining 6407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 8176 0.98 - 1.97: 419 1.97 - 2.95: 89 2.95 - 3.93: 28 3.93 - 4.92: 12 Bond angle restraints: 8724 Sorted by residual: angle pdb=" C VAL A 196 " pdb=" N ARG A 197 " pdb=" CA ARG A 197 " ideal model delta sigma weight residual 120.09 124.62 -4.53 1.25e+00 6.40e-01 1.31e+01 angle pdb=" C VAL B 196 " pdb=" N ARG B 197 " pdb=" CA ARG B 197 " ideal model delta sigma weight residual 120.09 124.61 -4.52 1.25e+00 6.40e-01 1.31e+01 angle pdb=" C VAL D 196 " pdb=" N ARG D 197 " pdb=" CA ARG D 197 " ideal model delta sigma weight residual 120.09 124.61 -4.52 1.25e+00 6.40e-01 1.31e+01 angle pdb=" C VAL C 196 " pdb=" N ARG C 197 " pdb=" CA ARG C 197 " ideal model delta sigma weight residual 120.09 124.58 -4.49 1.25e+00 6.40e-01 1.29e+01 angle pdb=" N VAL C 184 " pdb=" CA VAL C 184 " pdb=" C VAL C 184 " ideal model delta sigma weight residual 112.29 109.52 2.77 9.40e-01 1.13e+00 8.66e+00 ... (remaining 8719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3408 16.49 - 32.99: 256 32.99 - 49.48: 28 49.48 - 65.98: 8 65.98 - 82.47: 4 Dihedral angle restraints: 3704 sinusoidal: 1448 harmonic: 2256 Sorted by residual: dihedral pdb=" CA TRP B 149 " pdb=" C TRP B 149 " pdb=" N LEU B 150 " pdb=" CA LEU B 150 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TRP C 149 " pdb=" C TRP C 149 " pdb=" N LEU C 150 " pdb=" CA LEU C 150 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TRP D 149 " pdb=" C TRP D 149 " pdb=" N LEU D 150 " pdb=" CA LEU D 150 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 467 0.026 - 0.052: 286 0.052 - 0.078: 111 0.078 - 0.104: 24 0.104 - 0.131: 16 Chirality restraints: 904 Sorted by residual: chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE C 182 " pdb=" N ILE C 182 " pdb=" C ILE C 182 " pdb=" CB ILE C 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE D 182 " pdb=" N ILE D 182 " pdb=" C ILE D 182 " pdb=" CB ILE D 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 901 not shown) Planarity restraints: 1140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 197 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO D 198 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 197 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 198 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 198 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 198 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 197 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO C 198 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 198 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 198 " -0.022 5.00e-02 4.00e+02 ... (remaining 1137 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 36 2.48 - 3.09: 4537 3.09 - 3.69: 9955 3.69 - 4.30: 15215 4.30 - 4.90: 25365 Nonbonded interactions: 55108 Sorted by model distance: nonbonded pdb=" OD2 ASP C 183 " pdb="MN MN C 301 " model vdw 1.880 2.320 nonbonded pdb=" OD2 ASP B 183 " pdb="MN MN B 301 " model vdw 1.881 2.320 nonbonded pdb=" OD2 ASP D 183 " pdb="MN MN D 301 " model vdw 1.881 2.320 nonbonded pdb=" OD2 ASP A 183 " pdb="MN MN A 301 " model vdw 1.881 2.320 nonbonded pdb=" NE2 HIS D 50 " pdb="MN MN D 301 " model vdw 2.017 2.400 ... (remaining 55103 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.090 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: 0.020 Set scattering table: 0.010 Process input model: 5.130 Find NCS groups from input model: 0.040 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:5.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6412 Z= 0.183 Angle : 0.551 4.917 8724 Z= 0.324 Chirality : 0.039 0.131 904 Planarity : 0.004 0.039 1140 Dihedral : 11.977 82.471 2272 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.81 (0.29), residues: 784 helix: 0.78 (0.23), residues: 504 sheet: 1.20 (0.52), residues: 72 loop : -0.02 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.023 0.002 TYR C 69 PHE 0.005 0.001 PHE B 90 TRP 0.009 0.001 TRP A 147 HIS 0.004 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6412) covalent geometry : angle 0.55137 ( 8724) hydrogen bonds : bond 0.14553 ( 404) hydrogen bonds : angle 7.48488 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.208 Fit side-chains REVERT: A 70 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 124 ASP cc_start: 0.8531 (m-30) cc_final: 0.8160 (m-30) REVERT: A 200 TYR cc_start: 0.9364 (t80) cc_final: 0.9120 (t80) REVERT: B 70 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 124 ASP cc_start: 0.8508 (m-30) cc_final: 0.8105 (m-30) REVERT: B 200 TYR cc_start: 0.9356 (t80) cc_final: 0.9143 (t80) REVERT: C 70 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7924 (tm-30) REVERT: C 124 ASP cc_start: 0.8491 (m-30) cc_final: 0.8071 (m-30) REVERT: C 200 TYR cc_start: 0.9358 (t80) cc_final: 0.9097 (t80) REVERT: D 70 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7854 (tm-30) REVERT: D 124 ASP cc_start: 0.8481 (m-30) cc_final: 0.8072 (m-30) REVERT: D 200 TYR cc_start: 0.9355 (t80) cc_final: 0.9142 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.5187 time to fit residues: 70.5107 Evaluate side-chains 105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0020 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.086751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.078501 restraints weight = 12344.971| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.03 r_work: 0.2947 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6412 Z= 0.143 Angle : 0.526 4.939 8724 Z= 0.285 Chirality : 0.039 0.125 904 Planarity : 0.004 0.038 1140 Dihedral : 7.310 86.756 844 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.42 % Allowed : 8.39 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.13 (0.30), residues: 784 helix: 0.88 (0.22), residues: 508 sheet: 1.33 (0.55), residues: 80 loop : 0.49 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 123 TYR 0.010 0.001 TYR B 69 PHE 0.005 0.001 PHE D 101 TRP 0.009 0.001 TRP A 147 HIS 0.003 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6412) covalent geometry : angle 0.52555 ( 8724) hydrogen bonds : bond 0.04298 ( 404) hydrogen bonds : angle 5.74488 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.257 Fit side-chains REVERT: A 48 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8194 (tm-30) REVERT: A 70 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 200 TYR cc_start: 0.9407 (t80) cc_final: 0.9161 (t80) REVERT: B 48 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 70 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7820 (tm-30) REVERT: B 200 TYR cc_start: 0.9414 (t80) cc_final: 0.9164 (t80) REVERT: C 48 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8199 (tm-30) REVERT: C 70 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7826 (tm-30) REVERT: C 200 TYR cc_start: 0.9414 (t80) cc_final: 0.9165 (t80) REVERT: D 48 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8190 (tm-30) REVERT: D 70 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7791 (tm-30) REVERT: D 200 TYR cc_start: 0.9392 (t80) cc_final: 0.9143 (t80) outliers start: 9 outliers final: 4 residues processed: 151 average time/residue: 0.5287 time to fit residues: 83.4601 Evaluate side-chains 118 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 206 ASN C 206 ASN D 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079722 restraints weight = 12449.327| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.98 r_work: 0.3020 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6412 Z= 0.135 Angle : 0.503 4.953 8724 Z= 0.269 Chirality : 0.039 0.121 904 Planarity : 0.004 0.038 1140 Dihedral : 7.100 84.191 844 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.53 % Allowed : 11.39 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.13 (0.30), residues: 784 helix: 0.87 (0.22), residues: 508 sheet: 1.79 (0.63), residues: 72 loop : 0.34 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 216 TYR 0.008 0.001 TYR A 33 PHE 0.006 0.001 PHE B 101 TRP 0.008 0.001 TRP B 147 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6412) covalent geometry : angle 0.50310 ( 8724) hydrogen bonds : bond 0.03936 ( 404) hydrogen bonds : angle 5.51548 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.253 Fit side-chains REVERT: A 48 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8542 (tm-30) REVERT: A 70 GLN cc_start: 0.8520 (tm-30) cc_final: 0.7999 (tm-30) REVERT: A 200 TYR cc_start: 0.9571 (t80) cc_final: 0.9321 (t80) REVERT: A 211 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8340 (tp30) REVERT: B 48 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8543 (tm-30) REVERT: B 70 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 200 TYR cc_start: 0.9575 (t80) cc_final: 0.9333 (t80) REVERT: B 211 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8312 (tp30) REVERT: C 48 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8556 (tm-30) REVERT: C 70 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8025 (tm-30) REVERT: C 200 TYR cc_start: 0.9576 (t80) cc_final: 0.9329 (t80) REVERT: C 211 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8337 (tp30) REVERT: C 218 MET cc_start: 0.8475 (tpp) cc_final: 0.8273 (mpp) REVERT: D 48 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8543 (tm-30) REVERT: D 70 GLN cc_start: 0.8544 (tm-30) cc_final: 0.7992 (tm-30) REVERT: D 200 TYR cc_start: 0.9574 (t80) cc_final: 0.9327 (t80) REVERT: D 218 MET cc_start: 0.8469 (tpp) cc_final: 0.8265 (mpp) outliers start: 16 outliers final: 6 residues processed: 135 average time/residue: 0.5132 time to fit residues: 72.8200 Evaluate side-chains 110 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 106 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.0270 chunk 27 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.087184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.077572 restraints weight = 12505.396| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.36 r_work: 0.2920 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6412 Z= 0.126 Angle : 0.502 4.939 8724 Z= 0.268 Chirality : 0.039 0.121 904 Planarity : 0.004 0.038 1140 Dihedral : 7.089 84.068 844 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.48 % Allowed : 11.71 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.13 (0.29), residues: 784 helix: 0.89 (0.22), residues: 508 sheet: 1.55 (0.58), residues: 80 loop : 0.31 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 216 TYR 0.007 0.001 TYR A 33 PHE 0.005 0.001 PHE D 101 TRP 0.007 0.001 TRP B 147 HIS 0.002 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6412) covalent geometry : angle 0.50186 ( 8724) hydrogen bonds : bond 0.03690 ( 404) hydrogen bonds : angle 5.35031 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.172 Fit side-chains REVERT: A 48 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 70 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7730 (tm-30) REVERT: A 200 TYR cc_start: 0.9435 (t80) cc_final: 0.9174 (t80) REVERT: A 211 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8002 (tp30) REVERT: A 218 MET cc_start: 0.7990 (tpp) cc_final: 0.7738 (mpp) REVERT: B 48 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B 70 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7734 (tm-30) REVERT: B 119 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8406 (mp0) REVERT: B 200 TYR cc_start: 0.9436 (t80) cc_final: 0.9180 (t80) REVERT: B 211 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7963 (tp30) REVERT: C 48 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 70 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7778 (tm-30) REVERT: C 119 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8460 (mp0) REVERT: C 200 TYR cc_start: 0.9439 (t80) cc_final: 0.9178 (t80) REVERT: C 211 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7963 (tp30) REVERT: D 48 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8133 (tm-30) REVERT: D 70 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7757 (tm-30) REVERT: D 119 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8465 (mp0) REVERT: D 200 TYR cc_start: 0.9432 (t80) cc_final: 0.9173 (t80) outliers start: 22 outliers final: 20 residues processed: 133 average time/residue: 0.5238 time to fit residues: 73.2188 Evaluate side-chains 126 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 199 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.078873 restraints weight = 12647.961| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.02 r_work: 0.3000 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6412 Z= 0.151 Angle : 0.508 5.019 8724 Z= 0.270 Chirality : 0.040 0.123 904 Planarity : 0.004 0.036 1140 Dihedral : 7.020 82.930 844 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.64 % Allowed : 11.71 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.13 (0.29), residues: 784 helix: 0.93 (0.22), residues: 508 sheet: 1.56 (0.62), residues: 72 loop : 0.26 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.009 0.001 TYR C 33 PHE 0.006 0.001 PHE A 101 TRP 0.007 0.001 TRP A 147 HIS 0.003 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6412) covalent geometry : angle 0.50792 ( 8724) hydrogen bonds : bond 0.03869 ( 404) hydrogen bonds : angle 5.44578 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.244 Fit side-chains REVERT: A 70 GLN cc_start: 0.8483 (tm-30) cc_final: 0.7957 (tm-30) REVERT: A 200 TYR cc_start: 0.9566 (t80) cc_final: 0.9350 (t80) REVERT: A 211 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8333 (tp30) REVERT: B 48 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8581 (tm-30) REVERT: B 70 GLN cc_start: 0.8481 (tm-30) cc_final: 0.7954 (tm-30) REVERT: B 200 TYR cc_start: 0.9569 (t80) cc_final: 0.9357 (t80) REVERT: B 211 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8267 (tp30) REVERT: B 218 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8329 (mpp) REVERT: C 70 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8020 (tm-30) REVERT: C 200 TYR cc_start: 0.9569 (t80) cc_final: 0.9350 (t80) REVERT: C 211 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8272 (tp30) REVERT: C 218 MET cc_start: 0.8526 (tpp) cc_final: 0.8230 (mpp) REVERT: D 48 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8562 (tm-30) REVERT: D 70 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7977 (tm-30) REVERT: D 200 TYR cc_start: 0.9583 (t80) cc_final: 0.9360 (t80) REVERT: D 218 MET cc_start: 0.8507 (tpp) cc_final: 0.8171 (mpp) outliers start: 23 outliers final: 18 residues processed: 118 average time/residue: 0.5687 time to fit residues: 70.3819 Evaluate side-chains 122 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 199 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.086550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076378 restraints weight = 12641.463| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.34 r_work: 0.2911 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6412 Z= 0.147 Angle : 0.522 4.999 8724 Z= 0.278 Chirality : 0.039 0.119 904 Planarity : 0.004 0.036 1140 Dihedral : 7.025 82.832 844 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.96 % Allowed : 12.34 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.08 (0.29), residues: 784 helix: 0.89 (0.22), residues: 508 sheet: 1.55 (0.62), residues: 72 loop : 0.23 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 197 TYR 0.008 0.001 TYR C 33 PHE 0.005 0.001 PHE D 101 TRP 0.007 0.001 TRP B 147 HIS 0.003 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6412) covalent geometry : angle 0.52166 ( 8724) hydrogen bonds : bond 0.03781 ( 404) hydrogen bonds : angle 5.37271 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.177 Fit side-chains REVERT: A 70 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 200 TYR cc_start: 0.9458 (t80) cc_final: 0.9219 (t80) REVERT: A 211 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8081 (tp30) REVERT: A 218 MET cc_start: 0.8229 (tpp) cc_final: 0.7956 (mpp) REVERT: B 70 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7738 (tm-30) REVERT: B 200 TYR cc_start: 0.9452 (t80) cc_final: 0.9221 (t80) REVERT: B 211 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8058 (tp30) REVERT: B 218 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7875 (mpp) REVERT: C 70 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7805 (tm-30) REVERT: C 200 TYR cc_start: 0.9458 (t80) cc_final: 0.9220 (t80) REVERT: C 211 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8040 (tp30) REVERT: C 218 MET cc_start: 0.8185 (tpp) cc_final: 0.7817 (mpp) REVERT: D 70 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7782 (tm-30) REVERT: D 200 TYR cc_start: 0.9454 (t80) cc_final: 0.9219 (t80) REVERT: D 218 MET cc_start: 0.8226 (tpp) cc_final: 0.7855 (mpp) outliers start: 25 outliers final: 20 residues processed: 129 average time/residue: 0.5176 time to fit residues: 70.0543 Evaluate side-chains 125 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 199 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075429 restraints weight = 12743.607| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.36 r_work: 0.2875 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6412 Z= 0.155 Angle : 0.524 5.535 8724 Z= 0.279 Chirality : 0.040 0.120 904 Planarity : 0.004 0.036 1140 Dihedral : 7.006 82.701 844 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.48 % Allowed : 13.13 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.09 (0.29), residues: 784 helix: 0.92 (0.22), residues: 508 sheet: 1.47 (0.63), residues: 72 loop : 0.23 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.009 0.001 TYR C 33 PHE 0.006 0.001 PHE B 101 TRP 0.007 0.001 TRP B 147 HIS 0.003 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6412) covalent geometry : angle 0.52359 ( 8724) hydrogen bonds : bond 0.03882 ( 404) hydrogen bonds : angle 5.43319 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.237 Fit side-chains REVERT: A 70 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7705 (tm-30) REVERT: A 200 TYR cc_start: 0.9439 (t80) cc_final: 0.9231 (t80) REVERT: A 211 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8046 (tp30) REVERT: A 218 MET cc_start: 0.8084 (tpp) cc_final: 0.7749 (mpp) REVERT: B 70 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 119 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8392 (mp0) REVERT: B 200 TYR cc_start: 0.9437 (t80) cc_final: 0.9237 (t80) REVERT: B 211 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8005 (tp30) REVERT: C 70 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7740 (tm-30) REVERT: C 119 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8410 (mp0) REVERT: C 200 TYR cc_start: 0.9441 (t80) cc_final: 0.9237 (t80) REVERT: C 211 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7991 (tp30) REVERT: D 70 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7698 (tm-30) REVERT: D 119 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8412 (mp0) REVERT: D 200 TYR cc_start: 0.9435 (t80) cc_final: 0.9232 (t80) outliers start: 22 outliers final: 19 residues processed: 114 average time/residue: 0.5581 time to fit residues: 66.5819 Evaluate side-chains 123 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.084996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.075859 restraints weight = 12348.026| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.25 r_work: 0.2876 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6412 Z= 0.172 Angle : 0.547 5.593 8724 Z= 0.290 Chirality : 0.040 0.119 904 Planarity : 0.004 0.036 1140 Dihedral : 7.034 82.821 844 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.16 % Allowed : 13.92 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.06 (0.29), residues: 784 helix: 0.91 (0.22), residues: 508 sheet: 1.38 (0.62), residues: 72 loop : 0.21 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 123 TYR 0.009 0.001 TYR C 33 PHE 0.006 0.001 PHE B 101 TRP 0.007 0.001 TRP D 147 HIS 0.003 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6412) covalent geometry : angle 0.54658 ( 8724) hydrogen bonds : bond 0.03934 ( 404) hydrogen bonds : angle 5.46859 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.160 Fit side-chains REVERT: A 70 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 119 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8431 (mp0) REVERT: A 200 TYR cc_start: 0.9481 (t80) cc_final: 0.9274 (t80) REVERT: A 211 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8208 (tp30) REVERT: B 70 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7764 (tm-30) REVERT: B 119 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8488 (mp0) REVERT: B 200 TYR cc_start: 0.9460 (t80) cc_final: 0.9259 (t80) REVERT: B 211 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8132 (tp30) REVERT: C 70 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7814 (tm-30) REVERT: C 119 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8466 (mp0) REVERT: C 200 TYR cc_start: 0.9476 (t80) cc_final: 0.9269 (t80) REVERT: C 211 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8175 (tp30) REVERT: C 218 MET cc_start: 0.8092 (tpp) cc_final: 0.7781 (mpp) REVERT: D 70 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7773 (tm-30) REVERT: D 119 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8477 (mp0) REVERT: D 200 TYR cc_start: 0.9476 (t80) cc_final: 0.9274 (t80) REVERT: D 211 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8194 (tp30) REVERT: D 218 MET cc_start: 0.8103 (tpp) cc_final: 0.7847 (mpp) outliers start: 20 outliers final: 16 residues processed: 116 average time/residue: 0.5480 time to fit residues: 66.4906 Evaluate side-chains 120 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.086912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.077840 restraints weight = 12407.117| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.22 r_work: 0.2924 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6412 Z= 0.138 Angle : 0.524 7.413 8724 Z= 0.277 Chirality : 0.039 0.117 904 Planarity : 0.004 0.036 1140 Dihedral : 6.983 82.508 844 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.69 % Allowed : 13.92 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.12 (0.29), residues: 784 helix: 0.97 (0.22), residues: 508 sheet: 1.32 (0.63), residues: 72 loop : 0.22 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 197 TYR 0.007 0.001 TYR D 33 PHE 0.005 0.001 PHE B 101 TRP 0.007 0.001 TRP D 147 HIS 0.003 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6412) covalent geometry : angle 0.52361 ( 8724) hydrogen bonds : bond 0.03763 ( 404) hydrogen bonds : angle 5.35876 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.242 Fit side-chains REVERT: A 70 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 119 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8374 (mp0) REVERT: A 200 TYR cc_start: 0.9441 (t80) cc_final: 0.9240 (t80) REVERT: A 211 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8192 (OUTLIER) REVERT: B 70 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 119 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8415 (mp0) REVERT: B 211 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8045 (tp30) REVERT: C 70 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7760 (tm-30) REVERT: C 119 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8415 (mp0) REVERT: C 200 TYR cc_start: 0.9443 (t80) cc_final: 0.9241 (t80) REVERT: C 211 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8043 (tp30) REVERT: C 218 MET cc_start: 0.7994 (tpp) cc_final: 0.7621 (mpp) REVERT: D 70 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7785 (tm-30) REVERT: D 119 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8406 (mp0) REVERT: D 200 TYR cc_start: 0.9439 (t80) cc_final: 0.9238 (t80) REVERT: D 211 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8064 (tp30) REVERT: D 218 MET cc_start: 0.7998 (tpp) cc_final: 0.7738 (mpp) outliers start: 17 outliers final: 21 residues processed: 126 average time/residue: 0.5748 time to fit residues: 75.8195 Evaluate side-chains 126 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.085543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.076279 restraints weight = 12331.962| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.32 r_work: 0.2890 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6412 Z= 0.144 Angle : 0.551 8.638 8724 Z= 0.291 Chirality : 0.039 0.119 904 Planarity : 0.004 0.036 1140 Dihedral : 7.023 82.765 844 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.53 % Allowed : 14.56 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.15 (0.29), residues: 784 helix: 0.98 (0.22), residues: 508 sheet: 1.35 (0.63), residues: 72 loop : 0.27 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 197 TYR 0.012 0.001 TYR B 200 PHE 0.005 0.001 PHE B 101 TRP 0.007 0.001 TRP C 147 HIS 0.003 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6412) covalent geometry : angle 0.55120 ( 8724) hydrogen bonds : bond 0.03773 ( 404) hydrogen bonds : angle 5.35208 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.251 Fit side-chains REVERT: A 70 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7782 (tm-30) REVERT: A 119 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8372 (mp0) REVERT: A 200 TYR cc_start: 0.9419 (t80) cc_final: 0.9166 (t80) REVERT: A 211 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8149 (OUTLIER) REVERT: B 70 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 119 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8415 (mp0) REVERT: B 211 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8011 (tp30) REVERT: C 70 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7726 (tm-30) REVERT: C 119 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8422 (mp0) REVERT: C 200 TYR cc_start: 0.9420 (t80) cc_final: 0.9220 (t80) REVERT: C 211 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8022 (tp30) REVERT: C 218 MET cc_start: 0.8072 (tpp) cc_final: 0.7753 (mpp) REVERT: D 70 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7785 (tm-30) REVERT: D 119 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8425 (mp0) REVERT: D 211 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8004 (tp30) REVERT: D 218 MET cc_start: 0.8103 (tpp) cc_final: 0.7861 (mpp) outliers start: 16 outliers final: 17 residues processed: 120 average time/residue: 0.5324 time to fit residues: 67.1138 Evaluate side-chains 125 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.3980 chunk 57 optimal weight: 0.0870 chunk 73 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.085616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.076636 restraints weight = 12259.664| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.30 r_work: 0.2903 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6412 Z= 0.129 Angle : 0.516 5.957 8724 Z= 0.274 Chirality : 0.039 0.118 904 Planarity : 0.004 0.036 1140 Dihedral : 6.946 82.228 844 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.53 % Allowed : 14.87 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.20 (0.29), residues: 784 helix: 1.03 (0.22), residues: 508 sheet: 1.29 (0.63), residues: 72 loop : 0.29 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.011 0.001 TYR D 200 PHE 0.004 0.001 PHE C 101 TRP 0.007 0.001 TRP D 147 HIS 0.003 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6412) covalent geometry : angle 0.51554 ( 8724) hydrogen bonds : bond 0.03711 ( 404) hydrogen bonds : angle 5.29595 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1874.68 seconds wall clock time: 32 minutes 48.41 seconds (1968.41 seconds total)