Starting phenix.real_space_refine on Wed Mar 12 05:09:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vi3_43247/03_2025/8vi3_43247.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vi3_43247/03_2025/8vi3_43247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vi3_43247/03_2025/8vi3_43247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vi3_43247/03_2025/8vi3_43247.map" model { file = "/net/cci-nas-00/data/ceres_data/8vi3_43247/03_2025/8vi3_43247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vi3_43247/03_2025/8vi3_43247.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.017 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 27 5.16 5 C 4988 2.51 5 N 1140 2.21 5 O 1204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7359 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2455 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 308, 2452 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Conformer: "B" Number of residues, atoms: 308, 2452 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} bond proxies already assigned to first conformer: 2529 Chain: "B" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2452 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain: "C" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2452 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Time building chain proxies: 8.02, per 1000 atoms: 1.09 Number of scatterers: 7359 At special positions: 0 Unit cell: (97.352, 98.484, 62.26, 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 27 16.00 O 1204 8.00 N 1140 7.00 C 4988 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: 1.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 10 through 13 Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 36 through 66 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.636A pdb=" N SER A 81 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 101 through 124 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.585A pdb=" N THR A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.821A pdb=" N ALA A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 161 Processing helix chain 'A' and resid 162 through 192 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 194 through 199 removed outlier: 4.263A pdb=" N ALA A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.946A pdb=" N PHE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 249 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 277 removed outlier: 4.060A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 309 Processing helix chain 'B' and resid 10 through 13 Processing helix chain 'B' and resid 14 through 29 Processing helix chain 'B' and resid 36 through 66 Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.526A pdb=" N SER B 81 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 Processing helix chain 'B' and resid 101 through 124 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.651A pdb=" N THR B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 142 through 147 removed outlier: 3.769A pdb=" N ALA B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 162 through 192 Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 194 through 199 removed outlier: 4.310A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.948A pdb=" N PHE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 249 Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 277 removed outlier: 4.025A pdb=" N PHE B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 309 Processing helix chain 'C' and resid 10 through 13 Processing helix chain 'C' and resid 14 through 29 Processing helix chain 'C' and resid 36 through 66 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.620A pdb=" N SER C 81 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 98 Processing helix chain 'C' and resid 101 through 124 Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.677A pdb=" N THR C 138 " --> pdb=" O GLN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 142 through 147 removed outlier: 3.745A pdb=" N ALA C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 161 Processing helix chain 'C' and resid 162 through 191 Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 194 through 199 removed outlier: 4.332A pdb=" N ALA C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 205 through 219 removed outlier: 3.954A pdb=" N PHE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 249 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'C' and resid 258 through 277 removed outlier: 4.078A pdb=" N PHE C 262 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 309 575 hydrogen bonds defined for protein. 1634 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: 2.40 Time building geometry restraints manager: 2.18 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: 2154 1.34 - 1.46: 1884 1.46 - 1.58: 3514 1.58 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 7603 Sorted by residual: bond pdb=" N VAL B 223 " pdb=" CA VAL B 223 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.12e+00 bond pdb=" CA VAL A 223 " pdb=" CB VAL A 223 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.72e-01 bond pdb=" CB TRP B 231 " pdb=" CG TRP B 231 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.75e-01 bond pdb=" CB GLU C 68 " pdb=" CG GLU C 68 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.09e-01 bond pdb=" C ILE A 229 " pdb=" O ILE A 229 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.17e-02 7.31e+03 3.46e-01 ... (remaining 7598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 9999 0.91 - 1.82: 287 1.82 - 2.73: 39 2.73 - 3.64: 24 3.64 - 4.55: 23 Bond angle restraints: 10372 Sorted by residual: angle pdb=" N PHE B 7 " pdb=" CA PHE B 7 " pdb=" C PHE B 7 " ideal model delta sigma weight residual 109.72 113.77 -4.05 1.25e+00 6.40e-01 1.05e+01 angle pdb=" N VAL B 223 " pdb=" CA VAL B 223 " pdb=" C VAL B 223 " ideal model delta sigma weight residual 106.21 109.20 -2.99 1.07e+00 8.73e-01 7.79e+00 angle pdb=" N TRP B 231 " pdb=" CA TRP B 231 " pdb=" CB TRP B 231 " ideal model delta sigma weight residual 110.12 113.56 -3.44 1.47e+00 4.63e-01 5.48e+00 angle pdb=" CA VAL B 223 " pdb=" C VAL B 223 " pdb=" O VAL B 223 " ideal model delta sigma weight residual 122.63 120.86 1.77 8.70e-01 1.32e+00 4.13e+00 angle pdb=" N PHE B 7 " pdb=" CA PHE B 7 " pdb=" CB PHE B 7 " ideal model delta sigma weight residual 110.32 113.32 -3.00 1.48e+00 4.57e-01 4.11e+00 ... (remaining 10367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 3945 17.14 - 34.28: 267 34.28 - 51.42: 46 51.42 - 68.55: 12 68.55 - 85.69: 4 Dihedral angle restraints: 4274 sinusoidal: 1603 harmonic: 2671 Sorted by residual: dihedral pdb=" CB GLU A 222 " pdb=" CG GLU A 222 " pdb=" CD GLU A 222 " pdb=" OE1 GLU A 222 " ideal model delta sinusoidal sigma weight residual 0.00 85.69 -85.69 1 3.00e+01 1.11e-03 9.87e+00 dihedral pdb=" CB GLU A 134 " pdb=" CG GLU A 134 " pdb=" CD GLU A 134 " pdb=" OE1 GLU A 134 " ideal model delta sinusoidal sigma weight residual 0.00 -85.53 85.53 1 3.00e+01 1.11e-03 9.84e+00 dihedral pdb=" CB MET C 294 " pdb=" CG MET C 294 " pdb=" SD MET C 294 " pdb=" CE MET C 294 " ideal model delta sinusoidal sigma weight residual 180.00 122.96 57.04 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 4271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1029 0.060 - 0.121: 141 0.121 - 0.181: 0 0.181 - 0.241: 0 0.241 - 0.302: 1 Chirality restraints: 1171 Sorted by residual: chirality pdb=" CA PHE B 7 " pdb=" N PHE B 7 " pdb=" C PHE B 7 " pdb=" CB PHE B 7 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA VAL A 279 " pdb=" N VAL A 279 " pdb=" C VAL A 279 " pdb=" CB VAL A 279 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.17e-01 chirality pdb=" CA PRO A 207 " pdb=" N PRO A 207 " pdb=" C PRO A 207 " pdb=" CB PRO A 207 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.16e-01 ... (remaining 1168 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 231 " -0.028 2.00e-02 2.50e+03 1.91e-02 9.13e+00 pdb=" CG TRP B 231 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 231 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 231 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 231 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 231 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 231 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 231 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 231 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 231 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 231 " 0.022 2.00e-02 2.50e+03 1.35e-02 4.59e+00 pdb=" CG TRP A 231 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 231 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 231 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 231 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 231 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 231 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 231 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 231 " 0.021 2.00e-02 2.50e+03 1.30e-02 4.25e+00 pdb=" CG TRP C 231 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 231 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP C 231 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 231 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 231 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 231 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 231 " 0.001 2.00e-02 2.50e+03 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 306 2.73 - 3.27: 8129 3.27 - 3.81: 13372 3.81 - 4.36: 16264 4.36 - 4.90: 28185 Nonbonded interactions: 66256 Sorted by model distance: nonbonded pdb=" NE1 TRP A 177 " pdb=" OE1 GLU A 181 " model vdw 2.186 3.120 nonbonded pdb=" O THR B 121 " pdb=" OG SER B 125 " model vdw 2.189 3.040 nonbonded pdb=" O THR C 121 " pdb=" OG SER C 125 " model vdw 2.191 3.040 nonbonded pdb=" NE1 TRP B 177 " pdb=" OE1 GLU B 181 " model vdw 2.201 3.120 nonbonded pdb=" O THR A 121 " pdb=" OG SER A 125 " model vdw 2.222 3.040 ... (remaining 66251 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 283 or resid 285 through 313)) selection = (chain 'B' and (resid 6 through 283 or resid 285 through 313)) selection = (chain 'C' and (resid 6 through 283 or resid 285 through 313)) } 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=0.50 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: 23.540 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.170 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7603 Z= 0.118 Angle : 0.436 4.553 10372 Z= 0.236 Chirality : 0.036 0.302 1171 Planarity : 0.003 0.026 1258 Dihedral : 12.322 85.692 2568 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.29), residues: 919 helix: 2.02 (0.20), residues: 745 sheet: None (None), residues: 0 loop : 0.18 (0.53), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 231 HIS 0.002 0.001 HIS A 163 PHE 0.010 0.001 PHE B 34 TYR 0.007 0.001 TYR A 304 ARG 0.001 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.801 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 1.1272 time to fit residues: 102.1397 Evaluate side-chains 63 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 292 ASN B 29 HIS C 29 HIS C 163 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.091270 restraints weight = 11108.611| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.52 r_work: 0.2862 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7603 Z= 0.232 Angle : 0.513 6.197 10372 Z= 0.257 Chirality : 0.041 0.123 1171 Planarity : 0.004 0.037 1258 Dihedral : 3.796 16.737 992 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.17 % Allowed : 5.48 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.29), residues: 919 helix: 1.71 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.26 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 231 HIS 0.008 0.001 HIS B 29 PHE 0.012 0.001 PHE A 151 TYR 0.011 0.001 TYR B 304 ARG 0.005 0.001 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.883 Fit side-chains REVERT: A 42 ASP cc_start: 0.8901 (m-30) cc_final: 0.8666 (m-30) REVERT: A 219 ASN cc_start: 0.8383 (p0) cc_final: 0.8080 (p0) REVERT: B 219 ASN cc_start: 0.8438 (p0) cc_final: 0.8102 (p0) REVERT: B 222 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7872 (mt-10) REVERT: C 42 ASP cc_start: 0.8857 (m-30) cc_final: 0.8567 (m-30) REVERT: C 219 ASN cc_start: 0.8423 (p0) cc_final: 0.8179 (p0) outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 1.6469 time to fit residues: 145.5074 Evaluate side-chains 74 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 163 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.105676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.092468 restraints weight = 11397.286| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.59 r_work: 0.2857 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7603 Z= 0.207 Angle : 0.483 6.391 10372 Z= 0.242 Chirality : 0.039 0.118 1171 Planarity : 0.004 0.033 1258 Dihedral : 3.773 17.231 992 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.17 % Allowed : 6.27 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.28), residues: 919 helix: 1.91 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 1.04 (0.50), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 231 HIS 0.002 0.001 HIS A 187 PHE 0.010 0.001 PHE C 180 TYR 0.008 0.001 TYR A 143 ARG 0.007 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.860 Fit side-chains REVERT: A 42 ASP cc_start: 0.8882 (m-30) cc_final: 0.8652 (m-30) REVERT: C 42 ASP cc_start: 0.8878 (m-30) cc_final: 0.8568 (m-30) REVERT: C 219 ASN cc_start: 0.8392 (p0) cc_final: 0.8188 (p0) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 1.5040 time to fit residues: 127.5642 Evaluate side-chains 78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 42 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 HIS B 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.094224 restraints weight = 11268.638| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.58 r_work: 0.2884 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7603 Z= 0.164 Angle : 0.461 6.382 10372 Z= 0.230 Chirality : 0.038 0.116 1171 Planarity : 0.004 0.032 1258 Dihedral : 3.711 17.083 992 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.70 % Allowed : 6.53 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.28), residues: 919 helix: 1.68 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.23 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 231 HIS 0.002 0.001 HIS A 187 PHE 0.010 0.001 PHE C 180 TYR 0.015 0.001 TYR B 304 ARG 0.006 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.858 Fit side-chains REVERT: A 42 ASP cc_start: 0.8864 (m-30) cc_final: 0.8638 (m-30) REVERT: B 42 ASP cc_start: 0.8838 (m-30) cc_final: 0.8574 (m-30) REVERT: C 42 ASP cc_start: 0.8862 (m-30) cc_final: 0.8553 (m-30) outliers start: 13 outliers final: 7 residues processed: 85 average time/residue: 1.2104 time to fit residues: 109.9312 Evaluate side-chains 82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.108018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.095944 restraints weight = 9268.789| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.32 r_work: 0.2861 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7603 Z= 0.192 Angle : 0.471 6.520 10372 Z= 0.235 Chirality : 0.039 0.119 1171 Planarity : 0.004 0.030 1258 Dihedral : 3.733 17.298 992 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.44 % Allowed : 7.44 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.28), residues: 919 helix: 1.67 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.28 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 231 HIS 0.002 0.001 HIS B 187 PHE 0.009 0.001 PHE C 180 TYR 0.018 0.001 TYR B 61 ARG 0.006 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.742 Fit side-chains REVERT: A 42 ASP cc_start: 0.8736 (m-30) cc_final: 0.8504 (m-30) REVERT: B 42 ASP cc_start: 0.8747 (m-30) cc_final: 0.8472 (m-30) REVERT: C 42 ASP cc_start: 0.8763 (m-30) cc_final: 0.8459 (m-30) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 1.0394 time to fit residues: 92.7250 Evaluate side-chains 83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 80 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.110663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.097376 restraints weight = 11181.384| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.61 r_work: 0.2793 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7603 Z= 0.166 Angle : 0.456 6.572 10372 Z= 0.228 Chirality : 0.038 0.116 1171 Planarity : 0.004 0.031 1258 Dihedral : 3.688 17.178 992 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.44 % Allowed : 7.44 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.28), residues: 919 helix: 1.72 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.33 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 231 HIS 0.003 0.000 HIS B 187 PHE 0.009 0.001 PHE B 180 TYR 0.016 0.001 TYR B 304 ARG 0.007 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.806 Fit side-chains REVERT: A 42 ASP cc_start: 0.8723 (m-30) cc_final: 0.8503 (m-30) REVERT: B 42 ASP cc_start: 0.8712 (m-30) cc_final: 0.8441 (m-30) REVERT: C 42 ASP cc_start: 0.8756 (m-30) cc_final: 0.8449 (m-30) outliers start: 11 outliers final: 7 residues processed: 85 average time/residue: 1.0882 time to fit residues: 99.0369 Evaluate side-chains 85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 42 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.109974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.097185 restraints weight = 10923.366| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.50 r_work: 0.2876 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7603 Z= 0.152 Angle : 0.451 6.329 10372 Z= 0.225 Chirality : 0.038 0.115 1171 Planarity : 0.004 0.030 1258 Dihedral : 3.655 17.197 992 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.57 % Allowed : 7.44 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.28), residues: 919 helix: 1.78 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.39 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 231 HIS 0.002 0.000 HIS B 187 PHE 0.008 0.001 PHE C 180 TYR 0.015 0.001 TYR C 304 ARG 0.007 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.927 Fit side-chains REVERT: A 42 ASP cc_start: 0.8756 (m-30) cc_final: 0.8542 (m-30) REVERT: A 231 TRP cc_start: 0.8796 (OUTLIER) cc_final: 0.7852 (m-10) REVERT: B 42 ASP cc_start: 0.8730 (m-30) cc_final: 0.8458 (m-30) REVERT: C 42 ASP cc_start: 0.8789 (m-30) cc_final: 0.8465 (m-30) outliers start: 12 outliers final: 7 residues processed: 85 average time/residue: 1.1057 time to fit residues: 100.4595 Evaluate side-chains 85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 78 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.107486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.095117 restraints weight = 9214.600| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.39 r_work: 0.2793 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7603 Z= 0.241 Angle : 0.488 6.457 10372 Z= 0.245 Chirality : 0.039 0.127 1171 Planarity : 0.004 0.043 1258 Dihedral : 3.805 17.390 992 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.44 % Allowed : 8.09 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.28), residues: 919 helix: 1.69 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.33 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 231 HIS 0.002 0.001 HIS A 75 PHE 0.011 0.001 PHE A 262 TYR 0.016 0.001 TYR B 304 ARG 0.007 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.850 Fit side-chains REVERT: A 42 ASP cc_start: 0.8717 (m-30) cc_final: 0.8482 (m-30) REVERT: B 42 ASP cc_start: 0.8742 (m-30) cc_final: 0.8518 (m-30) REVERT: C 42 ASP cc_start: 0.8747 (m-30) cc_final: 0.8414 (m-30) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 1.0940 time to fit residues: 99.4021 Evaluate side-chains 84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.108460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.093927 restraints weight = 17010.896| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.97 r_work: 0.2870 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7603 Z= 0.166 Angle : 0.459 6.541 10372 Z= 0.231 Chirality : 0.038 0.117 1171 Planarity : 0.004 0.041 1258 Dihedral : 3.724 17.400 992 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.17 % Allowed : 8.36 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.28), residues: 919 helix: 1.70 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.41 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 231 HIS 0.001 0.000 HIS B 187 PHE 0.009 0.001 PHE C 180 TYR 0.013 0.001 TYR B 61 ARG 0.007 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.768 Fit side-chains REVERT: A 42 ASP cc_start: 0.8828 (m-30) cc_final: 0.8623 (m-30) REVERT: B 42 ASP cc_start: 0.8823 (m-30) cc_final: 0.8564 (m-30) REVERT: C 42 ASP cc_start: 0.8882 (m-30) cc_final: 0.8567 (m-30) REVERT: C 219 ASN cc_start: 0.8247 (p0) cc_final: 0.7865 (p0) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 1.0282 time to fit residues: 94.7096 Evaluate side-chains 85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 0.0370 chunk 52 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.108946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.094584 restraints weight = 16787.762| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.94 r_work: 0.2823 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7603 Z= 0.159 Angle : 0.455 5.798 10372 Z= 0.230 Chirality : 0.038 0.116 1171 Planarity : 0.004 0.032 1258 Dihedral : 3.681 17.229 992 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.04 % Allowed : 8.62 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.28), residues: 919 helix: 1.75 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.44 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 231 HIS 0.001 0.000 HIS A 187 PHE 0.010 0.001 PHE B 170 TYR 0.016 0.001 TYR C 61 ARG 0.007 0.000 ARG A 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.707 Fit side-chains REVERT: A 42 ASP cc_start: 0.8784 (m-30) cc_final: 0.8570 (m-30) REVERT: A 231 TRP cc_start: 0.8843 (OUTLIER) cc_final: 0.7944 (m-10) REVERT: B 42 ASP cc_start: 0.8758 (m-30) cc_final: 0.8458 (m-30) REVERT: C 42 ASP cc_start: 0.8822 (m-30) cc_final: 0.8500 (m-30) outliers start: 8 outliers final: 6 residues processed: 86 average time/residue: 1.0201 time to fit residues: 94.3069 Evaluate side-chains 85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 231 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.108902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.094409 restraints weight = 16997.626| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.97 r_work: 0.2794 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7603 Z= 0.169 Angle : 0.462 6.689 10372 Z= 0.232 Chirality : 0.038 0.117 1171 Planarity : 0.004 0.034 1258 Dihedral : 3.686 17.300 992 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.04 % Allowed : 8.88 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.28), residues: 919 helix: 1.73 (0.19), residues: 775 sheet: None (None), residues: 0 loop : 0.45 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 231 HIS 0.001 0.000 HIS B 187 PHE 0.009 0.001 PHE B 170 TYR 0.016 0.001 TYR C 61 ARG 0.007 0.000 ARG A 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5825.81 seconds wall clock time: 104 minutes 22.81 seconds (6262.81 seconds total)