Starting phenix.real_space_refine on Wed Sep 17 08:47:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vi5_43249/09_2025/8vi5_43249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vi5_43249/09_2025/8vi5_43249.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 { model { file = "/net/cci-nas-00/data/ceres_data/8vi5_43249/09_2025/8vi5_43249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vi5_43249/09_2025/8vi5_43249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vi5_43249/09_2025/8vi5_43249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vi5_43249/09_2025/8vi5_43249.map" } 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= 0.000 sd= 0.013 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 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.41, per 1000 atoms: 0.33 Number of scatterers: 7359 At special positions: 0 Unit cell: (91.126, 100.748, 61.694, 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: 0.67 Conformation dependent library (CDL) restraints added in 475.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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 89.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 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 79 through 83 removed outlier: 3.565A pdb=" N PHE A 82 " --> pdb=" O ARG A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 101 through 123 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.583A 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: 3.853A 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: 4.440A 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: 3.978A pdb=" N PHE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.522A 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: 4.176A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 4.442A 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 79 through 83 Processing helix chain 'B' and resid 84 through 98 Processing helix chain 'B' and resid 101 through 123 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.665A 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: 3.819A 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: 4.480A 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: 3.999A pdb=" N PHE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 249 removed outlier: 3.560A pdb=" N LYS B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) 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: 4.152A pdb=" N PHE B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 4.441A 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 79 through 83 removed outlier: 3.505A pdb=" N PHE C 82 " --> pdb=" O ARG C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 98 Processing helix chain 'C' and resid 101 through 123 Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.650A 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: 3.823A 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: 4.491A 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: 3.995A pdb=" N PHE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.507A 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: 4.107A pdb=" N PHE C 262 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 309 569 hydrogen bonds defined for protein. 1622 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: 1.15 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2010 1.33 - 1.45: 1457 1.45 - 1.57: 4085 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 7603 Sorted by residual: bond pdb=" N ARG B 243 " pdb=" CA ARG B 243 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.28e-02 6.10e+03 6.07e+00 bond pdb=" N ARG A 243 " pdb=" CA ARG A 243 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.33e-02 5.65e+03 5.79e+00 bond pdb=" N HIS A 163 " pdb=" CA HIS A 163 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.48e+00 bond pdb=" N HIS C 163 " pdb=" CA HIS C 163 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.23e-02 6.61e+03 5.35e+00 bond pdb=" N HIS B 163 " pdb=" CA HIS B 163 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.24e+00 ... (remaining 7598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 10089 1.20 - 2.40: 208 2.40 - 3.59: 47 3.59 - 4.79: 27 4.79 - 5.99: 1 Bond angle restraints: 10372 Sorted by residual: angle pdb=" CA PRO C 6 " pdb=" N PRO C 6 " pdb=" CD PRO C 6 " ideal model delta sigma weight residual 112.00 106.01 5.99 1.40e+00 5.10e-01 1.83e+01 angle pdb=" CA ARG A 64 " pdb=" C ARG A 64 " pdb=" O ARG A 64 " ideal model delta sigma weight residual 120.42 117.24 3.18 1.06e+00 8.90e-01 9.01e+00 angle pdb=" CA ARG A 71 " pdb=" C ARG A 71 " pdb=" O ARG A 71 " ideal model delta sigma weight residual 120.55 117.63 2.92 1.06e+00 8.90e-01 7.61e+00 angle pdb=" CA HIS A 163 " pdb=" C HIS A 163 " pdb=" O HIS A 163 " ideal model delta sigma weight residual 120.42 117.69 2.73 1.06e+00 8.90e-01 6.63e+00 angle pdb=" CA HIS C 163 " pdb=" C HIS C 163 " pdb=" O HIS C 163 " ideal model delta sigma weight residual 120.42 117.73 2.69 1.06e+00 8.90e-01 6.45e+00 ... (remaining 10367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 3918 17.03 - 34.06: 283 34.06 - 51.09: 55 51.09 - 68.11: 11 68.11 - 85.14: 7 Dihedral angle restraints: 4274 sinusoidal: 1603 harmonic: 2671 Sorted by residual: dihedral pdb=" CG ARG B 198 " pdb=" CD ARG B 198 " pdb=" NE ARG B 198 " pdb=" CZ ARG B 198 " ideal model delta sinusoidal sigma weight residual 90.00 132.90 -42.90 2 1.50e+01 4.44e-03 9.89e+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 -85.14 85.14 1 3.00e+01 1.11e-03 9.76e+00 dihedral pdb=" N PHE B 7 " pdb=" C PHE B 7 " pdb=" CA PHE B 7 " pdb=" CB PHE B 7 " ideal model delta harmonic sigma weight residual 122.80 130.58 -7.78 0 2.50e+00 1.60e-01 9.68e+00 ... (remaining 4271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1052 0.063 - 0.125: 115 0.125 - 0.188: 3 0.188 - 0.251: 0 0.251 - 0.314: 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 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ARG A 71 " pdb=" N ARG A 71 " pdb=" C ARG A 71 " pdb=" CB ARG A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA ARG C 243 " pdb=" N ARG C 243 " pdb=" C ARG C 243 " pdb=" CB ARG C 243 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1168 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 231 " 0.023 2.00e-02 2.50e+03 1.54e-02 5.90e+00 pdb=" CG TRP B 231 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 231 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 231 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 231 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 231 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 231 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 231 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 231 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 231 " 0.023 2.00e-02 2.50e+03 1.51e-02 5.68e+00 pdb=" CG TRP C 231 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 231 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 231 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 231 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 231 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 231 " 0.002 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 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 231 " 0.023 2.00e-02 2.50e+03 1.50e-02 5.66e+00 pdb=" CG TRP A 231 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 231 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 231 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 231 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 231 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 231 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 231 " 0.002 2.00e-02 2.50e+03 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 18 2.39 - 3.02: 4629 3.02 - 3.65: 11693 3.65 - 4.27: 18013 4.27 - 4.90: 30978 Nonbonded interactions: 65331 Sorted by model distance: nonbonded pdb=" OE1 GLU C 68 " pdb=" NH2 ARG C 71 " model vdw 1.764 3.120 nonbonded pdb=" O THR B 121 " pdb=" OG SER B 125 " model vdw 2.085 3.040 nonbonded pdb=" O THR C 121 " pdb=" OG SER C 125 " model vdw 2.097 3.040 nonbonded pdb=" OE1 GLU C 68 " pdb=" NH1 ARG C 71 " model vdw 2.172 3.120 nonbonded pdb=" O THR A 121 " pdb=" OG SER A 125 " model vdw 2.216 3.040 ... (remaining 65326 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: 6.470 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.360 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 0.032 7603 Z= 0.155 Angle : 0.494 5.991 10372 Z= 0.283 Chirality : 0.038 0.314 1171 Planarity : 0.003 0.025 1258 Dihedral : 12.933 85.142 2568 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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 aren not related in a simple way. whole: 2.79 (0.29), residues: 919 helix: 2.16 (0.20), residues: 718 sheet: None (None), residues: 0 loop : 0.85 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 71 TYR 0.007 0.001 TYR A 143 PHE 0.010 0.001 PHE C 262 TRP 0.041 0.002 TRP B 231 HIS 0.002 0.001 HIS B 276 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7603) covalent geometry : angle 0.49439 (10372) hydrogen bonds : bond 0.10709 ( 569) hydrogen bonds : angle 4.73737 ( 1622) *********************** 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 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.300 Fit side-chains REVERT: A 71 ARG cc_start: 0.7372 (mtm180) cc_final: 0.6396 (mmp-170) REVERT: B 255 ILE cc_start: 0.9325 (mm) cc_final: 0.8886 (mm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0911 time to fit residues: 9.8904 Evaluate side-chains 67 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.107019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.087998 restraints weight = 17139.120| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.23 r_work: 0.2717 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7603 Z= 0.132 Angle : 0.502 5.921 10372 Z= 0.253 Chirality : 0.039 0.128 1171 Planarity : 0.004 0.022 1258 Dihedral : 3.687 18.149 992 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.52 % Allowed : 4.70 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.29), residues: 919 helix: 1.88 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.48 (0.56), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.012 0.001 TYR A 66 PHE 0.013 0.001 PHE C 7 TRP 0.039 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7603) covalent geometry : angle 0.50172 (10372) hydrogen bonds : bond 0.03781 ( 569) hydrogen bonds : angle 4.07393 ( 1622) *********************** 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 76 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.223 Fit side-chains REVERT: A 71 ARG cc_start: 0.7171 (mtm180) cc_final: 0.5998 (tpt170) REVERT: B 39 MET cc_start: 0.7369 (tpp) cc_final: 0.7071 (tpp) REVERT: C 39 MET cc_start: 0.7294 (tpp) cc_final: 0.6981 (tpp) REVERT: C 103 LEU cc_start: 0.7799 (tt) cc_final: 0.7367 (mp) outliers start: 4 outliers final: 0 residues processed: 74 average time/residue: 0.0884 time to fit residues: 9.0347 Evaluate side-chains 69 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.105605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.088597 restraints weight = 11480.459| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.74 r_work: 0.2739 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1396 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= 0.138 Angle : 0.486 5.926 10372 Z= 0.242 Chirality : 0.039 0.128 1171 Planarity : 0.004 0.031 1258 Dihedral : 3.698 18.616 992 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.52 % Allowed : 4.83 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.28), residues: 919 helix: 1.96 (0.19), residues: 745 sheet: None (None), residues: 0 loop : 0.32 (0.53), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.011 0.001 TYR C 275 PHE 0.016 0.001 PHE A 7 TRP 0.031 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7603) covalent geometry : angle 0.48569 (10372) hydrogen bonds : bond 0.03697 ( 569) hydrogen bonds : angle 3.98661 ( 1622) *********************** 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 75 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.220 Fit side-chains REVERT: A 39 MET cc_start: 0.7313 (tpp) cc_final: 0.7002 (mmm) REVERT: A 71 ARG cc_start: 0.7195 (mtm180) cc_final: 0.5768 (mmp-170) REVERT: B 39 MET cc_start: 0.7439 (tpp) cc_final: 0.7006 (tpp) REVERT: C 39 MET cc_start: 0.7373 (tpp) cc_final: 0.6905 (tpp) REVERT: C 103 LEU cc_start: 0.7806 (tt) cc_final: 0.7378 (mp) outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 0.0907 time to fit residues: 9.2702 Evaluate side-chains 69 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 TRP 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 30 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 41 optimal weight: 0.0670 chunk 77 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3106 r_free = 0.3106 target = 0.107252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.090163 restraints weight = 11589.172| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.75 r_work: 0.2770 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7603 Z= 0.115 Angle : 0.461 5.825 10372 Z= 0.230 Chirality : 0.038 0.123 1171 Planarity : 0.004 0.044 1258 Dihedral : 3.655 18.516 992 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.78 % Allowed : 5.09 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.28), residues: 919 helix: 1.95 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.34 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.011 0.001 TYR C 275 PHE 0.010 0.001 PHE A 34 TRP 0.024 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7603) covalent geometry : angle 0.46141 (10372) hydrogen bonds : bond 0.03462 ( 569) hydrogen bonds : angle 3.88879 ( 1622) *********************** 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 83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.314 Fit side-chains REVERT: A 39 MET cc_start: 0.7395 (tpp) cc_final: 0.7049 (tpp) REVERT: A 71 ARG cc_start: 0.7208 (mtm180) cc_final: 0.5783 (mmt-90) REVERT: C 31 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7889 (mm-30) REVERT: C 39 MET cc_start: 0.7447 (tpp) cc_final: 0.6953 (tpp) REVERT: C 103 LEU cc_start: 0.7781 (tt) cc_final: 0.7315 (mp) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.0842 time to fit residues: 9.6775 Evaluate side-chains 77 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 231 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.109044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.090286 restraints weight = 17182.172| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.19 r_work: 0.2734 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7603 Z= 0.114 Angle : 0.464 7.298 10372 Z= 0.228 Chirality : 0.038 0.122 1171 Planarity : 0.004 0.048 1258 Dihedral : 3.632 18.448 992 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.65 % Allowed : 6.66 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.28), residues: 919 helix: 2.01 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.31 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.015 0.001 TYR A 275 PHE 0.011 0.001 PHE A 34 TRP 0.026 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7603) covalent geometry : angle 0.46358 (10372) hydrogen bonds : bond 0.03410 ( 569) hydrogen bonds : angle 3.85583 ( 1622) *********************** 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 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.275 Fit side-chains REVERT: A 39 MET cc_start: 0.7490 (tpp) cc_final: 0.7069 (tpp) REVERT: A 71 ARG cc_start: 0.7253 (mtm180) cc_final: 0.5810 (mmt-90) REVERT: B 39 MET cc_start: 0.7514 (tpp) cc_final: 0.6967 (tpp) REVERT: B 79 ARG cc_start: 0.7674 (mtp180) cc_final: 0.7412 (mtm-85) REVERT: C 31 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7901 (mm-30) REVERT: C 39 MET cc_start: 0.7531 (tpp) cc_final: 0.7023 (tpp) REVERT: C 103 LEU cc_start: 0.7793 (tt) cc_final: 0.7332 (mp) outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 0.0866 time to fit residues: 9.3174 Evaluate side-chains 76 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 231 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3109 r_free = 0.3109 target = 0.107474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.090571 restraints weight = 11135.966| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.70 r_work: 0.2776 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1746 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= 0.115 Angle : 0.462 6.756 10372 Z= 0.228 Chirality : 0.038 0.156 1171 Planarity : 0.004 0.049 1258 Dihedral : 3.611 18.577 992 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.65 % Allowed : 6.53 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.28), residues: 919 helix: 2.04 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.33 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 243 TYR 0.007 0.001 TYR B 233 PHE 0.012 0.001 PHE A 34 TRP 0.026 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7603) covalent geometry : angle 0.46165 (10372) hydrogen bonds : bond 0.03384 ( 569) hydrogen bonds : angle 3.85034 ( 1622) *********************** 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 82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.270 Fit side-chains REVERT: A 39 MET cc_start: 0.7440 (tpp) cc_final: 0.6978 (tpp) REVERT: A 71 ARG cc_start: 0.7212 (mtm180) cc_final: 0.5711 (mmp-170) REVERT: B 39 MET cc_start: 0.7515 (tpp) cc_final: 0.6918 (tpp) REVERT: B 79 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7339 (mtm-85) REVERT: C 31 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7851 (mm-30) REVERT: C 39 MET cc_start: 0.7471 (tpp) cc_final: 0.6943 (tpp) REVERT: C 103 LEU cc_start: 0.7772 (tt) cc_final: 0.7317 (mp) outliers start: 5 outliers final: 4 residues processed: 81 average time/residue: 0.0961 time to fit residues: 10.4712 Evaluate side-chains 77 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 231 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.090612 restraints weight = 13006.429| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.85 r_work: 0.2738 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1722 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= 0.131 Angle : 0.483 9.911 10372 Z= 0.236 Chirality : 0.039 0.125 1171 Planarity : 0.004 0.049 1258 Dihedral : 3.647 18.741 992 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.65 % Allowed : 7.05 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.28), residues: 919 helix: 2.08 (0.19), residues: 745 sheet: None (None), residues: 0 loop : 0.20 (0.52), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 243 TYR 0.008 0.001 TYR B 233 PHE 0.009 0.001 PHE B 28 TRP 0.029 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7603) covalent geometry : angle 0.48298 (10372) hydrogen bonds : bond 0.03485 ( 569) hydrogen bonds : angle 3.88509 ( 1622) *********************** 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 81 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.279 Fit side-chains REVERT: A 39 MET cc_start: 0.7498 (tpp) cc_final: 0.7023 (tpp) REVERT: A 71 ARG cc_start: 0.7243 (mtm180) cc_final: 0.5794 (mmt-90) REVERT: B 39 MET cc_start: 0.7616 (tpp) cc_final: 0.7390 (tpp) REVERT: B 79 ARG cc_start: 0.7704 (mtp180) cc_final: 0.7406 (mtm-85) REVERT: B 250 GLU cc_start: 0.8570 (tt0) cc_final: 0.8291 (tt0) REVERT: C 31 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7887 (mm-30) REVERT: C 39 MET cc_start: 0.7530 (tpp) cc_final: 0.7024 (tpp) REVERT: C 103 LEU cc_start: 0.7821 (tt) cc_final: 0.7360 (mp) outliers start: 5 outliers final: 4 residues processed: 81 average time/residue: 0.0935 time to fit residues: 10.3823 Evaluate side-chains 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 231 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.105998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.086777 restraints weight = 20468.016| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.45 r_work: 0.2693 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1762 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= 0.129 Angle : 0.483 9.399 10372 Z= 0.235 Chirality : 0.040 0.271 1171 Planarity : 0.004 0.049 1258 Dihedral : 3.643 18.801 992 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.52 % Allowed : 7.18 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.28), residues: 919 helix: 2.00 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.29 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.008 0.001 TYR B 233 PHE 0.013 0.001 PHE A 34 TRP 0.028 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7603) covalent geometry : angle 0.48336 (10372) hydrogen bonds : bond 0.03471 ( 569) hydrogen bonds : angle 3.88860 ( 1622) *********************** 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 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.241 Fit side-chains REVERT: A 39 MET cc_start: 0.7444 (tpp) cc_final: 0.6959 (tpp) REVERT: A 71 ARG cc_start: 0.7191 (mtm180) cc_final: 0.5768 (mmt-90) REVERT: B 31 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7851 (mt-10) REVERT: B 39 MET cc_start: 0.7554 (tpp) cc_final: 0.7300 (tpp) REVERT: B 79 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7323 (mtm-85) REVERT: C 31 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7836 (mm-30) REVERT: C 39 MET cc_start: 0.7450 (tpp) cc_final: 0.6963 (tpp) REVERT: C 103 LEU cc_start: 0.7794 (tt) cc_final: 0.7343 (mp) outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 0.0891 time to fit residues: 9.6318 Evaluate side-chains 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 231 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.106621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.088001 restraints weight = 17146.937| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.21 r_work: 0.2720 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1811 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= 0.119 Angle : 0.483 9.299 10372 Z= 0.234 Chirality : 0.039 0.236 1171 Planarity : 0.004 0.050 1258 Dihedral : 3.607 18.669 992 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.65 % Allowed : 6.92 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.28), residues: 919 helix: 2.03 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.27 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.007 0.001 TYR B 233 PHE 0.009 0.001 PHE B 28 TRP 0.027 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7603) covalent geometry : angle 0.48276 (10372) hydrogen bonds : bond 0.03405 ( 569) hydrogen bonds : angle 3.86131 ( 1622) *********************** 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 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.272 Fit side-chains REVERT: A 39 MET cc_start: 0.7543 (tpp) cc_final: 0.7053 (tpp) REVERT: A 71 ARG cc_start: 0.7186 (mtm180) cc_final: 0.5695 (mmp-170) REVERT: B 39 MET cc_start: 0.7622 (tpp) cc_final: 0.7370 (tpp) REVERT: B 79 ARG cc_start: 0.7645 (mtp180) cc_final: 0.7350 (mtm-85) REVERT: C 31 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7888 (mm-30) REVERT: C 39 MET cc_start: 0.7528 (tpp) cc_final: 0.7035 (tpp) REVERT: C 103 LEU cc_start: 0.7747 (tt) cc_final: 0.7304 (mp) outliers start: 5 outliers final: 5 residues processed: 78 average time/residue: 0.0911 time to fit residues: 9.6406 Evaluate side-chains 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 231 TRP Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 76 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.105892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.089115 restraints weight = 11097.383| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.68 r_work: 0.2754 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1827 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= 0.129 Angle : 0.486 9.288 10372 Z= 0.237 Chirality : 0.039 0.229 1171 Planarity : 0.004 0.051 1258 Dihedral : 3.626 18.712 992 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.65 % Allowed : 6.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.28), residues: 919 helix: 2.00 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.25 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.007 0.001 TYR B 233 PHE 0.012 0.001 PHE A 34 TRP 0.028 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7603) covalent geometry : angle 0.48650 (10372) hydrogen bonds : bond 0.03464 ( 569) hydrogen bonds : angle 3.87993 ( 1622) ********************** 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 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.283 Fit side-chains REVERT: A 39 MET cc_start: 0.7533 (tpp) cc_final: 0.7030 (tpp) REVERT: A 71 ARG cc_start: 0.7194 (mtm180) cc_final: 0.5750 (mmt-90) REVERT: B 39 MET cc_start: 0.7609 (tpp) cc_final: 0.7347 (tpp) REVERT: B 79 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7334 (mtm-85) REVERT: C 31 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7863 (mm-30) REVERT: C 39 MET cc_start: 0.7509 (tpp) cc_final: 0.7013 (tpp) REVERT: C 103 LEU cc_start: 0.7783 (tt) cc_final: 0.7329 (mp) outliers start: 5 outliers final: 5 residues processed: 78 average time/residue: 0.0910 time to fit residues: 9.6449 Evaluate side-chains 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 231 TRP Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.105879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.087703 restraints weight = 15826.685| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.09 r_work: 0.2718 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1821 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= 0.130 Angle : 0.491 9.211 10372 Z= 0.240 Chirality : 0.039 0.217 1171 Planarity : 0.004 0.051 1258 Dihedral : 3.636 18.712 992 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.65 % Allowed : 6.92 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.28), residues: 919 helix: 1.99 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.25 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.008 0.001 TYR B 233 PHE 0.008 0.001 PHE B 28 TRP 0.028 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7603) covalent geometry : angle 0.49089 (10372) hydrogen bonds : bond 0.03465 ( 569) hydrogen bonds : angle 3.88863 ( 1622) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.60 seconds wall clock time: 36 minutes 43.30 seconds (2203.30 seconds total)