Starting phenix.real_space_refine on Mon Apr 28 09:36:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vi5_43249/04_2025/8vi5_43249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vi5_43249/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vi5_43249/04_2025/8vi5_43249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vi5_43249/04_2025/8vi5_43249.map" model { file = "/net/cci-nas-00/data/ceres_data/8vi5_43249/04_2025/8vi5_43249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vi5_43249/04_2025/8vi5_43249.cif" } resolution = 3.2 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 6.65, per 1000 atoms: 0.90 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: 1.88 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 89.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 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: 2.18 Time building geometry restraints manager: 2.23 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: 4.830 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.980 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- 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 : 4.66 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 (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: 2.79 (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 TRP 0.041 0.002 TRP B 231 HIS 0.002 0.001 HIS B 276 PHE 0.010 0.001 PHE C 262 TYR 0.007 0.001 TYR A 143 ARG 0.002 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.10709 ( 569) hydrogen bonds : angle 4.73737 ( 1622) covalent geometry : bond 0.00290 ( 7603) covalent geometry : angle 0.49439 (10372) *********************** 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 : 0.775 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: 0.2054 time to fit residues: 22.2847 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 : 0.680 ------------------------------------------------------------------------------- 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: 0.5980 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 C 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.106154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.089016 restraints weight = 11032.945| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.71 r_work: 0.2746 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7603 Z= 0.139 Angle : 0.504 5.919 10372 Z= 0.253 Chirality : 0.040 0.130 1171 Planarity : 0.004 0.023 1258 Dihedral : 3.678 17.983 992 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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 (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: 2.45 (0.29), residues: 919 helix: 1.95 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 0.36 (0.53), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 PHE 0.014 0.001 PHE C 7 TYR 0.013 0.001 TYR A 66 ARG 0.002 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 569) hydrogen bonds : angle 4.11956 ( 1622) covalent geometry : bond 0.00337 ( 7603) covalent geometry : angle 0.50394 (10372) *********************** 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 : 0.820 Fit side-chains REVERT: A 71 ARG cc_start: 0.7099 (mtm180) cc_final: 0.5971 (tpt170) REVERT: B 39 MET cc_start: 0.7260 (tpp) cc_final: 0.6991 (tpp) REVERT: C 39 MET cc_start: 0.7166 (tpp) cc_final: 0.6893 (tpp) REVERT: C 103 LEU cc_start: 0.7785 (tt) cc_final: 0.7347 (mp) outliers start: 4 outliers final: 0 residues processed: 74 average time/residue: 0.2176 time to fit residues: 22.5539 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 : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3092 r_free = 0.3092 target = 0.106399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.089258 restraints weight = 11599.363| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.75 r_work: 0.2755 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 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 = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1411 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= 0.129 Angle : 0.480 5.900 10372 Z= 0.239 Chirality : 0.039 0.125 1171 Planarity : 0.004 0.030 1258 Dihedral : 3.678 18.400 992 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.52 % Allowed : 5.09 % Favored : 94.39 % 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: 2.43 (0.28), residues: 919 helix: 1.88 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.47 (0.56), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 PHE 0.017 0.001 PHE A 7 TYR 0.010 0.001 TYR C 275 ARG 0.003 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 569) hydrogen bonds : angle 3.96872 ( 1622) covalent geometry : bond 0.00315 ( 7603) covalent geometry : angle 0.47987 (10372) *********************** 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 : 0.829 Fit side-chains REVERT: A 39 MET cc_start: 0.7301 (tpp) cc_final: 0.6987 (mmm) REVERT: A 71 ARG cc_start: 0.7171 (mtm180) cc_final: 0.5738 (mmp-170) REVERT: B 39 MET cc_start: 0.7414 (tpp) cc_final: 0.6989 (tpp) REVERT: C 39 MET cc_start: 0.7383 (tpp) cc_final: 0.6918 (tpp) REVERT: C 103 LEU cc_start: 0.7777 (tt) cc_final: 0.7350 (mp) outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.1983 time to fit residues: 20.3321 Evaluate side-chains 71 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TRP 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 51 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 81 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3076 r_free = 0.3076 target = 0.104976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.087870 restraints weight = 11579.957| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.73 r_work: 0.2733 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- 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 = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7603 Z= 0.145 Angle : 0.486 5.934 10372 Z= 0.242 Chirality : 0.039 0.130 1171 Planarity : 0.004 0.044 1258 Dihedral : 3.731 18.863 992 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.04 % Allowed : 5.35 % Favored : 93.60 % 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: 2.40 (0.28), residues: 919 helix: 1.94 (0.19), residues: 745 sheet: None (None), residues: 0 loop : 0.21 (0.52), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 PHE 0.010 0.001 PHE A 7 TYR 0.011 0.001 TYR A 275 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 569) hydrogen bonds : angle 3.96800 ( 1622) covalent geometry : bond 0.00361 ( 7603) covalent geometry : angle 0.48573 (10372) *********************** 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 84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.037 Fit side-chains REVERT: A 39 MET cc_start: 0.7358 (tpp) cc_final: 0.6987 (tpp) REVERT: A 71 ARG cc_start: 0.7213 (mtm180) cc_final: 0.5814 (mmt-90) REVERT: C 31 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7899 (mm-30) REVERT: C 39 MET cc_start: 0.7402 (tpp) cc_final: 0.6910 (tpp) REVERT: C 103 LEU cc_start: 0.7780 (tt) cc_final: 0.7298 (mp) outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.2183 time to fit residues: 24.2260 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 : 0.720 ------------------------------------------------------------------------------- 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 9 LEU 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: 1.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 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 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.105380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.089297 restraints weight = 9385.993| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.49 r_work: 0.2765 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1599 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= 0.134 Angle : 0.473 5.894 10372 Z= 0.236 Chirality : 0.039 0.127 1171 Planarity : 0.004 0.046 1258 Dihedral : 3.716 18.830 992 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.78 % Allowed : 6.53 % 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 (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: 2.40 (0.28), residues: 919 helix: 1.89 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.25 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 PHE 0.008 0.001 PHE C 180 TYR 0.009 0.001 TYR A 275 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 569) hydrogen bonds : angle 3.93134 ( 1622) covalent geometry : bond 0.00330 ( 7603) covalent geometry : angle 0.47281 (10372) *********************** 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 82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 1.003 Fit side-chains REVERT: A 39 MET cc_start: 0.7391 (tpp) cc_final: 0.6940 (tpp) REVERT: A 71 ARG cc_start: 0.7183 (mtm180) cc_final: 0.5781 (mmt-90) REVERT: B 39 MET cc_start: 0.7413 (tpp) cc_final: 0.6856 (tpp) REVERT: C 31 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7842 (mm-30) REVERT: C 39 MET cc_start: 0.7472 (tpp) cc_final: 0.6961 (tpp) REVERT: C 57 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7486 (mm) REVERT: C 103 LEU cc_start: 0.7793 (tt) cc_final: 0.7328 (mp) outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.3321 time to fit residues: 37.6597 Evaluate side-chains 81 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 9 LEU Chi-restraints excluded: chain C residue 57 LEU 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: 0.9990 chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3095 r_free = 0.3095 target = 0.106144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.089293 restraints weight = 11553.834| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.68 r_work: 0.2738 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7603 Z= 0.142 Angle : 0.476 5.914 10372 Z= 0.238 Chirality : 0.039 0.140 1171 Planarity : 0.004 0.049 1258 Dihedral : 3.721 18.944 992 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.78 % Allowed : 6.79 % 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 (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: 2.45 (0.28), residues: 919 helix: 1.98 (0.19), residues: 745 sheet: None (None), residues: 0 loop : 0.19 (0.52), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 PHE 0.011 0.001 PHE A 34 TYR 0.008 0.001 TYR B 233 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 569) hydrogen bonds : angle 3.93878 ( 1622) covalent geometry : bond 0.00350 ( 7603) covalent geometry : angle 0.47614 (10372) *********************** 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 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.807 Fit side-chains REVERT: A 39 MET cc_start: 0.7471 (tpp) cc_final: 0.6989 (tpp) REVERT: A 71 ARG cc_start: 0.7280 (mtm180) cc_final: 0.5855 (mmt-90) REVERT: B 39 MET cc_start: 0.7556 (tpp) cc_final: 0.7347 (tpp) REVERT: C 31 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7895 (mm-30) REVERT: C 39 MET cc_start: 0.7541 (tpp) cc_final: 0.7034 (tpp) REVERT: C 103 LEU cc_start: 0.7859 (tt) cc_final: 0.7388 (mp) outliers start: 6 outliers final: 6 residues processed: 78 average time/residue: 0.2069 time to fit residues: 22.2366 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 231 TRP Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 57 LEU 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: 2.9990 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.107878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.091083 restraints weight = 11050.772| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.65 r_work: 0.2766 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 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 = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1727 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= 0.119 Angle : 0.458 5.845 10372 Z= 0.229 Chirality : 0.039 0.128 1171 Planarity : 0.004 0.050 1258 Dihedral : 3.650 18.700 992 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.91 % Allowed : 6.66 % 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 (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: 2.53 (0.28), residues: 919 helix: 1.99 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.30 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 PHE 0.009 0.001 PHE B 28 TYR 0.013 0.001 TYR C 275 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 569) hydrogen bonds : angle 3.86698 ( 1622) covalent geometry : bond 0.00285 ( 7603) covalent geometry : angle 0.45844 (10372) *********************** 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 86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.755 Fit side-chains REVERT: A 39 MET cc_start: 0.7463 (tpp) cc_final: 0.6968 (tpp) REVERT: A 71 ARG cc_start: 0.7205 (mtm180) cc_final: 0.5753 (mmp-170) REVERT: B 39 MET cc_start: 0.7567 (tpp) cc_final: 0.7336 (tpp) REVERT: B 79 ARG cc_start: 0.7654 (mtp180) cc_final: 0.7362 (mtm-85) REVERT: C 31 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7873 (mm-30) REVERT: C 39 MET cc_start: 0.7520 (tpp) cc_final: 0.7011 (tpp) REVERT: C 103 LEU cc_start: 0.7795 (tt) cc_final: 0.7341 (mp) outliers start: 7 outliers final: 7 residues processed: 84 average time/residue: 0.4169 time to fit residues: 46.8856 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 : 2.061 ------------------------------------------------------------------------------- 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 9 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 231 TRP Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 60 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN C 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.105445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.089378 restraints weight = 9387.080| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.51 r_work: 0.2766 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1747 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= 0.132 Angle : 0.477 7.647 10372 Z= 0.236 Chirality : 0.039 0.130 1171 Planarity : 0.004 0.051 1258 Dihedral : 3.669 18.868 992 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.78 % Allowed : 6.53 % 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 (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 (0.28), residues: 919 helix: 1.97 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.29 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 PHE 0.012 0.001 PHE A 34 TYR 0.011 0.001 TYR C 275 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 569) hydrogen bonds : angle 3.89483 ( 1622) covalent geometry : bond 0.00323 ( 7603) covalent geometry : angle 0.47737 (10372) *********************** 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: 6 poor density : 74 time to evaluate : 0.984 Fit side-chains REVERT: A 39 MET cc_start: 0.7480 (tpp) cc_final: 0.6987 (tpp) REVERT: A 71 ARG cc_start: 0.7214 (mtm180) cc_final: 0.5805 (mmt-90) REVERT: B 39 MET cc_start: 0.7580 (tpp) cc_final: 0.7334 (tpp) REVERT: B 79 ARG cc_start: 0.7670 (mtp180) cc_final: 0.7364 (mtm-85) REVERT: C 31 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7876 (mm-30) REVERT: C 39 MET cc_start: 0.7487 (tpp) cc_final: 0.7000 (tpp) REVERT: C 103 LEU cc_start: 0.7820 (tt) cc_final: 0.7364 (mp) outliers start: 6 outliers final: 6 residues processed: 79 average time/residue: 0.3383 time to fit residues: 37.3906 Evaluate side-chains 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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 9 LEU Chi-restraints excluded: chain C residue 57 LEU 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: 1.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3093 r_free = 0.3093 target = 0.106249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.087658 restraints weight = 17284.818| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.22 r_work: 0.2715 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 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 = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1808 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= 0.121 Angle : 0.472 7.318 10372 Z= 0.233 Chirality : 0.039 0.128 1171 Planarity : 0.004 0.051 1258 Dihedral : 3.629 18.773 992 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 : 0.91 % Allowed : 6.66 % 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 (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: 2.56 (0.28), residues: 919 helix: 2.01 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.28 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 PHE 0.008 0.001 PHE B 28 TYR 0.011 0.001 TYR C 275 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 569) hydrogen bonds : angle 3.85899 ( 1622) covalent geometry : bond 0.00293 ( 7603) covalent geometry : angle 0.47224 (10372) *********************** 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 82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.766 Fit side-chains REVERT: A 39 MET cc_start: 0.7516 (tpp) cc_final: 0.7015 (tpp) REVERT: A 71 ARG cc_start: 0.7182 (mtm180) cc_final: 0.5717 (mmp-170) REVERT: B 39 MET cc_start: 0.7620 (tpp) cc_final: 0.7367 (tpp) REVERT: B 79 ARG cc_start: 0.7644 (mtp180) cc_final: 0.7344 (mtm-85) REVERT: B 250 GLU cc_start: 0.8586 (tt0) cc_final: 0.8273 (tt0) REVERT: C 31 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7889 (mm-30) REVERT: C 39 MET cc_start: 0.7523 (tpp) cc_final: 0.7028 (tpp) REVERT: C 103 LEU cc_start: 0.7781 (tt) cc_final: 0.7331 (mp) outliers start: 7 outliers final: 7 residues processed: 80 average time/residue: 0.2001 time to fit residues: 22.0493 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 : 0.692 ------------------------------------------------------------------------------- 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 9 LEU Chi-restraints excluded: chain C residue 57 LEU 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: 0.6980 chunk 52 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN C 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.106788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.088098 restraints weight = 16960.580| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.20 r_work: 0.2721 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1854 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 : 0.466 7.389 10372 Z= 0.230 Chirality : 0.038 0.127 1171 Planarity : 0.004 0.051 1258 Dihedral : 3.611 18.751 992 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.78 % Allowed : 6.66 % 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: 2.59 (0.29), residues: 919 helix: 2.03 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.29 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 231 HIS 0.002 0.001 HIS A 187 PHE 0.008 0.001 PHE C 180 TYR 0.011 0.001 TYR C 275 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 569) hydrogen bonds : angle 3.84817 ( 1622) covalent geometry : bond 0.00273 ( 7603) covalent geometry : angle 0.46586 (10372) ********************** 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 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.764 Fit side-chains REVERT: A 39 MET cc_start: 0.7577 (tpp) cc_final: 0.7076 (tpp) REVERT: A 71 ARG cc_start: 0.7246 (mtm180) cc_final: 0.5754 (mmp-170) REVERT: B 39 MET cc_start: 0.7651 (tpp) cc_final: 0.7402 (tpp) REVERT: B 79 ARG cc_start: 0.7687 (mtp180) cc_final: 0.7393 (mtm-85) REVERT: B 250 GLU cc_start: 0.8605 (tt0) cc_final: 0.8279 (tt0) REVERT: C 31 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7908 (mm-30) REVERT: C 39 MET cc_start: 0.7551 (tpp) cc_final: 0.7061 (tpp) REVERT: C 103 LEU cc_start: 0.7808 (tt) cc_final: 0.7362 (mp) outliers start: 6 outliers final: 5 residues processed: 79 average time/residue: 0.1923 time to fit residues: 20.9786 Evaluate side-chains 78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 57 LEU 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: 0.2980 chunk 47 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 24 optimal weight: 0.0030 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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 = 0.3114 r_free = 0.3114 target = 0.107960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.089381 restraints weight = 17130.214| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.21 r_work: 0.2740 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- 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 = 0.12 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 = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7603 Z= 0.106 Angle : 0.476 11.220 10372 Z= 0.230 Chirality : 0.038 0.126 1171 Planarity : 0.004 0.051 1258 Dihedral : 3.565 18.671 992 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 5.13 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 (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: 2.67 (0.29), residues: 919 helix: 2.08 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.34 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 231 HIS 0.003 0.001 HIS A 187 PHE 0.008 0.001 PHE C 180 TYR 0.011 0.001 TYR C 275 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 569) hydrogen bonds : angle 3.81372 ( 1622) covalent geometry : bond 0.00248 ( 7603) covalent geometry : angle 0.47618 (10372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4850.01 seconds wall clock time: 87 minutes 25.86 seconds (5245.86 seconds total)