Starting phenix.real_space_refine on Tue Mar 3 17:39:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qsy_53344/03_2026/9qsy_53344.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qsy_53344/03_2026/9qsy_53344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qsy_53344/03_2026/9qsy_53344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qsy_53344/03_2026/9qsy_53344.map" model { file = "/net/cci-nas-00/data/ceres_data/9qsy_53344/03_2026/9qsy_53344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qsy_53344/03_2026/9qsy_53344.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5020 2.51 5 N 1232 2.21 5 O 1284 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7576 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1893 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 12, 'TRANS': 238} Chain: "B" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1893 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 12, 'TRANS': 238} Chain: "C" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1893 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 12, 'TRANS': 238} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1893 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 12, 'TRANS': 238} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.98, per 1000 atoms: 0.26 Number of scatterers: 7576 At special positions: 0 Unit cell: (87.15, 87.15, 67.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1284 8.00 N 1232 7.00 C 5020 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: 0.72 Conformation dependent library (CDL) restraints added in 327.9 milliseconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 19 through 49 removed outlier: 3.620A pdb=" N ARG A 23 " --> pdb=" O TYR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.634A pdb=" N ILE A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 4.031A pdb=" N SER A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 99 through 123 removed outlier: 3.887A pdb=" N ILE A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 156 through 179 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 215 through 230 Proline residue: A 222 - end of helix removed outlier: 3.508A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.551A pdb=" N VAL A 235 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 244 through 265 Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 266 through 269 removed outlier: 3.519A pdb=" N LEU A 269 " --> pdb=" O GLY A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'B' and resid 20 through 49 Processing helix chain 'B' and resid 55 through 74 removed outlier: 3.634A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 4.032A pdb=" N SER B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'B' and resid 99 through 123 removed outlier: 3.885A pdb=" N ILE B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 156 through 179 Processing helix chain 'B' and resid 190 through 206 Processing helix chain 'B' and resid 215 through 230 Proline residue: B 222 - end of helix removed outlier: 3.506A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.550A pdb=" N VAL B 235 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 244 through 265 Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 266 through 269 removed outlier: 3.519A pdb=" N LEU B 269 " --> pdb=" O GLY B 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 269' Processing helix chain 'C' and resid 20 through 49 Processing helix chain 'C' and resid 55 through 74 removed outlier: 3.634A pdb=" N ILE C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 removed outlier: 4.033A pdb=" N SER C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 Processing helix chain 'C' and resid 99 through 123 removed outlier: 3.885A pdb=" N ILE C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 143 through 147 Processing helix chain 'C' and resid 156 through 179 Processing helix chain 'C' and resid 190 through 206 Processing helix chain 'C' and resid 215 through 230 Proline residue: C 222 - end of helix removed outlier: 3.508A pdb=" N LEU C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C 230 " --> pdb=" O THR C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.550A pdb=" N VAL C 235 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 244 through 265 Proline residue: C 250 - end of helix Processing helix chain 'C' and resid 266 through 269 removed outlier: 3.519A pdb=" N LEU C 269 " --> pdb=" O GLY C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'D' and resid 20 through 49 Processing helix chain 'D' and resid 55 through 74 removed outlier: 3.634A pdb=" N ILE D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 4.033A pdb=" N SER D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 99 through 123 removed outlier: 3.885A pdb=" N ILE D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 Processing helix chain 'D' and resid 143 through 147 Processing helix chain 'D' and resid 156 through 179 Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 215 through 230 Proline residue: D 222 - end of helix removed outlier: 3.506A pdb=" N LEU D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.550A pdb=" N VAL D 235 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 244 through 265 Proline residue: D 250 - end of helix Processing helix chain 'D' and resid 266 through 269 removed outlier: 3.529A pdb=" N LEU D 269 " --> pdb=" O GLY D 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 269' 532 hydrogen bonds defined for protein. 1560 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: 1.31 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2340 1.34 - 1.46: 1679 1.46 - 1.57: 3721 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 7800 Sorted by residual: bond pdb=" CB VAL A 201 " pdb=" CG2 VAL A 201 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.28e-01 bond pdb=" CB VAL B 201 " pdb=" CG2 VAL B 201 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.81e-01 bond pdb=" CB VAL D 201 " pdb=" CG2 VAL D 201 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.81e-01 bond pdb=" CB VAL C 201 " pdb=" CG2 VAL C 201 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.78e-01 bond pdb=" CB MET B 37 " pdb=" CG MET B 37 " ideal model delta sigma weight residual 1.520 1.497 0.023 3.00e-02 1.11e+03 5.72e-01 ... (remaining 7795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 10558 1.67 - 3.33: 82 3.33 - 5.00: 24 5.00 - 6.66: 0 6.66 - 8.33: 4 Bond angle restraints: 10668 Sorted by residual: angle pdb=" CA LEU D 35 " pdb=" CB LEU D 35 " pdb=" CG LEU D 35 " ideal model delta sigma weight residual 116.30 124.63 -8.33 3.50e+00 8.16e-02 5.67e+00 angle pdb=" CA LEU B 35 " pdb=" CB LEU B 35 " pdb=" CG LEU B 35 " ideal model delta sigma weight residual 116.30 124.62 -8.32 3.50e+00 8.16e-02 5.66e+00 angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 124.60 -8.30 3.50e+00 8.16e-02 5.62e+00 angle pdb=" CA LEU C 35 " pdb=" CB LEU C 35 " pdb=" CG LEU C 35 " ideal model delta sigma weight residual 116.30 124.54 -8.24 3.50e+00 8.16e-02 5.55e+00 angle pdb=" C VAL A 214 " pdb=" N ASN A 215 " pdb=" CA ASN A 215 " ideal model delta sigma weight residual 121.76 124.78 -3.02 1.74e+00 3.30e-01 3.02e+00 ... (remaining 10663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.65: 3481 10.65 - 21.30: 455 21.30 - 31.95: 210 31.95 - 42.59: 124 42.59 - 53.24: 46 Dihedral angle restraints: 4316 sinusoidal: 1532 harmonic: 2784 Sorted by residual: dihedral pdb=" CA GLN B 164 " pdb=" CB GLN B 164 " pdb=" CG GLN B 164 " pdb=" CD GLN B 164 " ideal model delta sinusoidal sigma weight residual -180.00 -126.76 -53.24 3 1.50e+01 4.44e-03 9.19e+00 dihedral pdb=" CA GLN C 164 " pdb=" CB GLN C 164 " pdb=" CG GLN C 164 " pdb=" CD GLN C 164 " ideal model delta sinusoidal sigma weight residual -180.00 -126.79 -53.21 3 1.50e+01 4.44e-03 9.19e+00 dihedral pdb=" CA GLN A 164 " pdb=" CB GLN A 164 " pdb=" CG GLN A 164 " pdb=" CD GLN A 164 " ideal model delta sinusoidal sigma weight residual -180.00 -126.80 -53.20 3 1.50e+01 4.44e-03 9.18e+00 ... (remaining 4313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 656 0.027 - 0.053: 376 0.053 - 0.080: 127 0.080 - 0.106: 49 0.106 - 0.133: 12 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CB VAL C 214 " pdb=" CA VAL C 214 " pdb=" CG1 VAL C 214 " pdb=" CG2 VAL C 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CB VAL A 214 " pdb=" CA VAL A 214 " pdb=" CG1 VAL A 214 " pdb=" CG2 VAL A 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CB VAL B 214 " pdb=" CA VAL B 214 " pdb=" CG1 VAL B 214 " pdb=" CG2 VAL B 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1217 not shown) Planarity restraints: 1340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 113 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C PHE B 113 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE B 113 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 114 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 113 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C PHE C 113 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE C 113 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU C 114 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 113 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C PHE A 113 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE A 113 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 114 " -0.010 2.00e-02 2.50e+03 ... (remaining 1337 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 4981 3.04 - 3.50: 8199 3.50 - 3.97: 12203 3.97 - 4.43: 15517 4.43 - 4.90: 23816 Nonbonded interactions: 64716 Sorted by model distance: nonbonded pdb=" C SER C 78 " pdb=" OG SER C 78 " model vdw 2.571 2.616 nonbonded pdb=" C SER B 78 " pdb=" OG SER B 78 " model vdw 2.571 2.616 nonbonded pdb=" C SER D 78 " pdb=" OG SER D 78 " model vdw 2.572 2.616 nonbonded pdb=" C SER A 78 " pdb=" OG SER A 78 " model vdw 2.572 2.616 nonbonded pdb=" N THR A 238 " pdb=" OG1 THR A 238 " model vdw 2.645 2.496 ... (remaining 64711 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: 1.450 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.003 0.026 7800 Z= 0.145 Angle : 0.495 8.331 10668 Z= 0.263 Chirality : 0.040 0.133 1220 Planarity : 0.005 0.040 1340 Dihedral : 14.616 53.242 2564 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.55 % Allowed : 18.65 % Favored : 79.79 % 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: 0.40 (0.25), residues: 996 helix: 1.09 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -1.53 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 188 TYR 0.009 0.001 TYR D 261 PHE 0.012 0.001 PHE B 165 TRP 0.004 0.001 TRP A 242 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7800) covalent geometry : angle 0.49550 (10668) hydrogen bonds : bond 0.11784 ( 532) hydrogen bonds : angle 6.58957 ( 1560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.268 Fit side-chains REVERT: A 37 MET cc_start: 0.6975 (ttt) cc_final: 0.6721 (ttp) REVERT: A 238 THR cc_start: 0.8664 (m) cc_final: 0.8287 (p) REVERT: B 238 THR cc_start: 0.8735 (m) cc_final: 0.8470 (p) REVERT: C 238 THR cc_start: 0.8517 (m) cc_final: 0.8295 (p) REVERT: D 170 SER cc_start: 0.7618 (m) cc_final: 0.7037 (p) REVERT: D 233 SER cc_start: 0.7970 (m) cc_final: 0.7518 (t) outliers start: 12 outliers final: 2 residues processed: 81 average time/residue: 0.0725 time to fit residues: 8.7863 Evaluate side-chains 62 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.171406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.131442 restraints weight = 7203.333| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.02 r_work: 0.3240 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7800 Z= 0.135 Angle : 0.516 8.927 10668 Z= 0.262 Chirality : 0.040 0.151 1220 Planarity : 0.004 0.043 1340 Dihedral : 3.830 20.269 1062 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.11 % Allowed : 15.16 % Favored : 81.74 % 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: 1.36 (0.26), residues: 996 helix: 1.96 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 188 TYR 0.009 0.001 TYR A 104 PHE 0.013 0.001 PHE B 165 TRP 0.006 0.001 TRP B 231 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7800) covalent geometry : angle 0.51564 (10668) hydrogen bonds : bond 0.03891 ( 532) hydrogen bonds : angle 4.37698 ( 1560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.6753 (m110) REVERT: A 240 GLN cc_start: 0.7146 (tm-30) cc_final: 0.6882 (tm-30) REVERT: B 90 MET cc_start: 0.6535 (mmt) cc_final: 0.6142 (mmp) REVERT: C 238 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8248 (p) REVERT: D 233 SER cc_start: 0.7954 (m) cc_final: 0.7529 (t) outliers start: 24 outliers final: 18 residues processed: 74 average time/residue: 0.0731 time to fit residues: 8.0785 Evaluate side-chains 72 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 254 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 97 optimal weight: 0.0470 chunk 44 optimal weight: 0.0010 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4284 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.176836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136512 restraints weight = 7004.934| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.07 r_work: 0.3293 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7800 Z= 0.103 Angle : 0.457 8.309 10668 Z= 0.228 Chirality : 0.038 0.126 1220 Planarity : 0.004 0.041 1340 Dihedral : 3.463 14.673 1060 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.68 % Allowed : 16.84 % Favored : 81.48 % 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: 1.82 (0.26), residues: 996 helix: 2.33 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.46 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.005 0.001 TYR A 261 PHE 0.014 0.001 PHE C 165 TRP 0.003 0.000 TRP D 128 HIS 0.002 0.000 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7800) covalent geometry : angle 0.45698 (10668) hydrogen bonds : bond 0.03439 ( 532) hydrogen bonds : angle 4.19003 ( 1560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.252 Fit side-chains REVERT: A 240 GLN cc_start: 0.7157 (tm-30) cc_final: 0.6910 (tm-30) REVERT: B 264 MET cc_start: 0.7962 (mmm) cc_final: 0.7711 (mmm) REVERT: C 238 THR cc_start: 0.8641 (m) cc_final: 0.8346 (p) outliers start: 13 outliers final: 9 residues processed: 57 average time/residue: 0.0689 time to fit residues: 6.1302 Evaluate side-chains 53 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 249 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 71 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.166993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.127222 restraints weight = 7309.985| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.03 r_work: 0.3217 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7800 Z= 0.137 Angle : 0.505 9.032 10668 Z= 0.252 Chirality : 0.040 0.128 1220 Planarity : 0.004 0.042 1340 Dihedral : 3.602 14.977 1060 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.98 % Allowed : 16.97 % Favored : 80.05 % 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: 1.62 (0.26), residues: 996 helix: 2.21 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -1.52 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.010 0.001 TYR A 261 PHE 0.013 0.001 PHE C 165 TRP 0.004 0.001 TRP D 242 HIS 0.002 0.000 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7800) covalent geometry : angle 0.50532 (10668) hydrogen bonds : bond 0.03871 ( 532) hydrogen bonds : angle 4.18418 ( 1560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 44 time to evaluate : 0.233 Fit side-chains REVERT: A 170 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7269 (p) REVERT: A 240 GLN cc_start: 0.7346 (tm-30) cc_final: 0.6996 (tm-30) REVERT: B 170 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7197 (p) REVERT: B 209 ASN cc_start: 0.7527 (OUTLIER) cc_final: 0.7181 (m110) REVERT: C 170 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7173 (p) REVERT: D 170 SER cc_start: 0.7852 (OUTLIER) cc_final: 0.7150 (p) REVERT: D 209 ASN cc_start: 0.7350 (OUTLIER) cc_final: 0.7002 (m-40) outliers start: 23 outliers final: 15 residues processed: 67 average time/residue: 0.0653 time to fit residues: 6.8023 Evaluate side-chains 63 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 254 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 38 optimal weight: 0.0000 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.166971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.127920 restraints weight = 7309.707| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.98 r_work: 0.3225 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7800 Z= 0.133 Angle : 0.494 8.571 10668 Z= 0.246 Chirality : 0.040 0.127 1220 Planarity : 0.004 0.043 1340 Dihedral : 3.681 15.488 1060 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.46 % Allowed : 17.88 % Favored : 79.66 % 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: 1.59 (0.26), residues: 996 helix: 2.12 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.47 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 188 TYR 0.008 0.001 TYR D 261 PHE 0.013 0.001 PHE C 165 TRP 0.004 0.001 TRP D 242 HIS 0.002 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7800) covalent geometry : angle 0.49382 (10668) hydrogen bonds : bond 0.03789 ( 532) hydrogen bonds : angle 4.13936 ( 1560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.248 Fit side-chains REVERT: A 170 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7126 (p) REVERT: B 170 SER cc_start: 0.7978 (OUTLIER) cc_final: 0.7197 (p) REVERT: B 209 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7270 (m110) REVERT: C 170 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7134 (p) REVERT: D 209 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7164 (m-40) outliers start: 19 outliers final: 12 residues processed: 64 average time/residue: 0.0675 time to fit residues: 6.6935 Evaluate side-chains 64 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 249 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 0.9980 chunk 56 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.0070 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 0.0010 chunk 2 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.3402 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.171372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.132117 restraints weight = 7209.616| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.02 r_work: 0.3263 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7800 Z= 0.092 Angle : 0.454 9.039 10668 Z= 0.225 Chirality : 0.038 0.121 1220 Planarity : 0.004 0.042 1340 Dihedral : 3.475 14.376 1060 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.68 % Allowed : 18.65 % Favored : 79.66 % 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 (0.27), residues: 996 helix: 2.48 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -1.33 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.005 0.001 TYR A 124 PHE 0.013 0.001 PHE C 165 TRP 0.004 0.000 TRP C 243 HIS 0.002 0.000 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 7800) covalent geometry : angle 0.45397 (10668) hydrogen bonds : bond 0.03248 ( 532) hydrogen bonds : angle 4.00124 ( 1560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.165 Fit side-chains REVERT: B 209 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7197 (m110) REVERT: C 238 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8286 (p) REVERT: D 170 SER cc_start: 0.7807 (OUTLIER) cc_final: 0.7097 (p) REVERT: D 209 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7100 (m-40) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 0.0736 time to fit residues: 5.5765 Evaluate side-chains 48 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 249 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.167362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127633 restraints weight = 7269.176| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.03 r_work: 0.3202 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7800 Z= 0.123 Angle : 0.488 8.734 10668 Z= 0.241 Chirality : 0.039 0.127 1220 Planarity : 0.004 0.043 1340 Dihedral : 3.561 14.689 1060 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.33 % Allowed : 17.62 % Favored : 80.05 % 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: 1.80 (0.27), residues: 996 helix: 2.21 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -1.29 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.008 0.001 TYR A 261 PHE 0.013 0.001 PHE C 165 TRP 0.003 0.001 TRP D 242 HIS 0.001 0.000 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7800) covalent geometry : angle 0.48764 (10668) hydrogen bonds : bond 0.03654 ( 532) hydrogen bonds : angle 4.06043 ( 1560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.267 Fit side-chains REVERT: B 170 SER cc_start: 0.7882 (OUTLIER) cc_final: 0.7137 (p) REVERT: B 209 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7248 (m110) REVERT: C 170 SER cc_start: 0.7832 (OUTLIER) cc_final: 0.7120 (p) REVERT: C 238 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8242 (p) REVERT: D 170 SER cc_start: 0.7907 (OUTLIER) cc_final: 0.7188 (p) REVERT: D 209 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7121 (m-40) outliers start: 18 outliers final: 12 residues processed: 63 average time/residue: 0.0678 time to fit residues: 6.6057 Evaluate side-chains 66 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 254 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 71 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 94 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.170996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.131307 restraints weight = 7180.266| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.04 r_work: 0.3279 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7800 Z= 0.096 Angle : 0.464 8.416 10668 Z= 0.228 Chirality : 0.038 0.122 1220 Planarity : 0.004 0.042 1340 Dihedral : 3.466 14.201 1060 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.33 % Allowed : 17.75 % Favored : 79.92 % 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: 1.93 (0.27), residues: 996 helix: 2.35 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -1.35 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.005 0.001 TYR A 124 PHE 0.012 0.001 PHE C 165 TRP 0.003 0.000 TRP C 243 HIS 0.001 0.000 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 7800) covalent geometry : angle 0.46404 (10668) hydrogen bonds : bond 0.03310 ( 532) hydrogen bonds : angle 3.97600 ( 1560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.248 Fit side-chains REVERT: A 96 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7747 (tt0) REVERT: A 170 SER cc_start: 0.7850 (OUTLIER) cc_final: 0.7106 (p) REVERT: B 53 HIS cc_start: 0.6718 (t-90) cc_final: 0.5642 (t-90) REVERT: B 170 SER cc_start: 0.7828 (OUTLIER) cc_final: 0.7094 (p) REVERT: B 209 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7191 (m110) REVERT: B 264 MET cc_start: 0.8179 (mmm) cc_final: 0.7930 (mmm) REVERT: C 170 SER cc_start: 0.7759 (OUTLIER) cc_final: 0.7049 (p) REVERT: C 238 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8283 (p) REVERT: D 170 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7110 (p) REVERT: D 209 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.7253 (m-40) REVERT: D 264 MET cc_start: 0.8261 (mmm) cc_final: 0.7885 (mmm) outliers start: 18 outliers final: 10 residues processed: 53 average time/residue: 0.0696 time to fit residues: 5.7096 Evaluate side-chains 53 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 254 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.169891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130368 restraints weight = 7140.516| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.03 r_work: 0.3243 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7800 Z= 0.113 Angle : 0.479 8.551 10668 Z= 0.235 Chirality : 0.039 0.137 1220 Planarity : 0.004 0.041 1340 Dihedral : 3.491 14.423 1060 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.33 % Allowed : 17.88 % Favored : 79.79 % 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: 1.83 (0.27), residues: 996 helix: 2.23 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -1.35 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.007 0.001 TYR C 261 PHE 0.012 0.001 PHE D 165 TRP 0.002 0.000 TRP B 242 HIS 0.001 0.000 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7800) covalent geometry : angle 0.47924 (10668) hydrogen bonds : bond 0.03499 ( 532) hydrogen bonds : angle 4.00693 ( 1560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.190 Fit side-chains REVERT: A 53 HIS cc_start: 0.6768 (t-90) cc_final: 0.5856 (t-90) REVERT: A 170 SER cc_start: 0.7880 (OUTLIER) cc_final: 0.7131 (p) REVERT: B 53 HIS cc_start: 0.6805 (t-90) cc_final: 0.5676 (t-90) REVERT: B 170 SER cc_start: 0.7873 (OUTLIER) cc_final: 0.7135 (p) REVERT: B 209 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.7365 (m110) REVERT: B 264 MET cc_start: 0.8208 (mmm) cc_final: 0.7960 (mmm) REVERT: C 170 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.7112 (p) REVERT: D 170 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7143 (p) REVERT: D 209 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.7280 (m-40) REVERT: D 264 MET cc_start: 0.8306 (mmm) cc_final: 0.8018 (mmm) outliers start: 18 outliers final: 12 residues processed: 58 average time/residue: 0.0680 time to fit residues: 6.0749 Evaluate side-chains 59 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 254 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.170168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130230 restraints weight = 7177.345| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.07 r_work: 0.3243 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7800 Z= 0.105 Angle : 0.469 8.378 10668 Z= 0.230 Chirality : 0.038 0.124 1220 Planarity : 0.004 0.042 1340 Dihedral : 3.459 14.153 1060 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.20 % Allowed : 18.01 % Favored : 79.79 % 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: 1.90 (0.27), residues: 996 helix: 2.30 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -1.34 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.006 0.001 TYR C 261 PHE 0.012 0.001 PHE C 165 TRP 0.002 0.000 TRP A 243 HIS 0.001 0.000 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7800) covalent geometry : angle 0.46914 (10668) hydrogen bonds : bond 0.03393 ( 532) hydrogen bonds : angle 3.96761 ( 1560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.244 Fit side-chains REVERT: A 53 HIS cc_start: 0.6759 (t-90) cc_final: 0.6111 (t-90) REVERT: A 170 SER cc_start: 0.7850 (OUTLIER) cc_final: 0.7109 (p) REVERT: B 53 HIS cc_start: 0.6865 (t-90) cc_final: 0.5723 (t-90) REVERT: B 170 SER cc_start: 0.7832 (OUTLIER) cc_final: 0.7094 (p) REVERT: B 209 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.7197 (m110) REVERT: B 264 MET cc_start: 0.8205 (mmm) cc_final: 0.7961 (mmm) REVERT: C 170 SER cc_start: 0.7781 (OUTLIER) cc_final: 0.7065 (p) REVERT: D 170 SER cc_start: 0.7823 (OUTLIER) cc_final: 0.7100 (p) REVERT: D 209 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.7234 (m-40) REVERT: D 264 MET cc_start: 0.8277 (mmm) cc_final: 0.7986 (mmm) outliers start: 17 outliers final: 11 residues processed: 55 average time/residue: 0.0681 time to fit residues: 5.7208 Evaluate side-chains 56 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 254 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 0.0040 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 82 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.170121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130375 restraints weight = 7189.502| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.06 r_work: 0.3258 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7800 Z= 0.109 Angle : 0.476 8.510 10668 Z= 0.233 Chirality : 0.039 0.127 1220 Planarity : 0.004 0.041 1340 Dihedral : 3.458 14.314 1060 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.46 % Allowed : 17.75 % Favored : 79.79 % 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: 1.88 (0.27), residues: 996 helix: 2.28 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.007 0.001 TYR C 261 PHE 0.012 0.001 PHE C 165 TRP 0.002 0.000 TRP D 128 HIS 0.001 0.000 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7800) covalent geometry : angle 0.47574 (10668) hydrogen bonds : bond 0.03461 ( 532) hydrogen bonds : angle 3.99354 ( 1560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1459.87 seconds wall clock time: 25 minutes 51.10 seconds (1551.10 seconds total)