Starting phenix.real_space_refine on Wed Mar 12 14:21:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukc_26576/03_2025/7ukc_26576.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukc_26576/03_2025/7ukc_26576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ukc_26576/03_2025/7ukc_26576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukc_26576/03_2025/7ukc_26576.map" model { file = "/net/cci-nas-00/data/ceres_data/7ukc_26576/03_2025/7ukc_26576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukc_26576/03_2025/7ukc_26576.cif" } resolution = 3.0 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= 0.005 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 56 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8000 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, D Time building chain proxies: 6.50, per 1000 atoms: 0.81 Number of scatterers: 8000 At special positions: 0 Unit cell: (108.206, 106.554, 83.426, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 56 16.00 O 1356 8.00 N 1332 7.00 C 5252 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: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 280 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 306 removed outlier: 3.507A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 321 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 3.939A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.640A pdb=" N LEU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.538A pdb=" N TYR C 225 " --> pdb=" O CYS C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 278 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 298 through 307 removed outlier: 3.802A pdb=" N LYS C 302 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 347 removed outlier: 5.359A pdb=" N SER C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.844A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 400 through 423 removed outlier: 4.419A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 280 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.507A pdb=" N ARG D 305 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 Processing helix chain 'D' and resid 321 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.939A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 removed outlier: 3.640A pdb=" N LEU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 424 Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.538A pdb=" N TYR A 225 " --> pdb=" O CYS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 278 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.803A pdb=" N LYS A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 347 removed outlier: 5.359A pdb=" N SER A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.844A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 400 through 423 removed outlier: 4.420A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1815 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: 2.15 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2436 1.34 - 1.46: 1525 1.46 - 1.57: 4139 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8188 Sorted by residual: bond pdb=" CB GLU C 346 " pdb=" CG GLU C 346 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB GLU A 346 " pdb=" CG GLU A 346 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CG GLU A 346 " pdb=" CD GLU A 346 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CG GLU C 346 " pdb=" CD GLU C 346 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CB LEU D 371 " pdb=" CG LEU D 371 " ideal model delta sigma weight residual 1.530 1.504 0.026 2.00e-02 2.50e+03 1.63e+00 ... (remaining 8183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10814 1.68 - 3.37: 244 3.37 - 5.05: 52 5.05 - 6.74: 8 6.74 - 8.42: 6 Bond angle restraints: 11124 Sorted by residual: angle pdb=" C PHE A 175 " pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 122.38 114.93 7.45 1.81e+00 3.05e-01 1.70e+01 angle pdb=" C PHE C 175 " pdb=" N GLU C 176 " pdb=" CA GLU C 176 " ideal model delta sigma weight residual 122.38 114.93 7.45 1.81e+00 3.05e-01 1.69e+01 angle pdb=" C ILE B 270 " pdb=" CA ILE B 270 " pdb=" CB ILE B 270 " ideal model delta sigma weight residual 111.65 107.18 4.47 1.41e+00 5.03e-01 1.00e+01 angle pdb=" C ILE D 270 " pdb=" CA ILE D 270 " pdb=" CB ILE D 270 " ideal model delta sigma weight residual 111.65 107.20 4.45 1.41e+00 5.03e-01 9.98e+00 angle pdb=" N GLU A 176 " pdb=" CA GLU A 176 " pdb=" CB GLU A 176 " ideal model delta sigma weight residual 110.44 114.14 -3.70 1.53e+00 4.27e-01 5.84e+00 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 4334 16.23 - 32.46: 376 32.46 - 48.69: 72 48.69 - 64.93: 6 64.93 - 81.16: 4 Dihedral angle restraints: 4792 sinusoidal: 1760 harmonic: 3032 Sorted by residual: dihedral pdb=" CA ARG C 293 " pdb=" C ARG C 293 " pdb=" N VAL C 294 " pdb=" CA VAL C 294 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ARG A 293 " pdb=" C ARG A 293 " pdb=" N VAL A 294 " pdb=" CA VAL A 294 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA THR A 370 " pdb=" C THR A 370 " pdb=" N LEU A 371 " pdb=" CA LEU A 371 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 793 0.035 - 0.070: 388 0.070 - 0.106: 92 0.106 - 0.141: 43 0.141 - 0.176: 4 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA GLU B 176 " pdb=" N GLU B 176 " pdb=" C GLU B 176 " pdb=" CB GLU B 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA GLU D 176 " pdb=" N GLU D 176 " pdb=" C GLU D 176 " pdb=" CB GLU D 176 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA PHE C 194 " pdb=" N PHE C 194 " pdb=" C PHE C 194 " pdb=" CB PHE C 194 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 1317 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 172 " 0.020 2.00e-02 2.50e+03 1.61e-02 6.51e+00 pdb=" CG TRP B 172 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 172 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 172 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 172 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 172 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 172 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 172 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 172 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 172 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 172 " -0.020 2.00e-02 2.50e+03 1.61e-02 6.47e+00 pdb=" CG TRP D 172 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 172 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 172 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 172 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 172 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 172 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 172 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 172 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 172 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 346 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" CD GLU D 346 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU D 346 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU D 346 " -0.010 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.73: 661 2.73 - 3.33: 10452 3.33 - 3.93: 15425 3.93 - 4.54: 21774 4.54 - 5.14: 32004 Nonbonded interactions: 80316 Sorted by model distance: nonbonded pdb=" OH TYR C 188 " pdb=" O HIS C 306 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" O HIS A 306 " model vdw 2.128 3.040 nonbonded pdb=" OE2 GLU D 205 " pdb=" NH2 ARG D 293 " model vdw 2.282 3.120 nonbonded pdb=" OE2 GLU B 205 " pdb=" NH2 ARG B 293 " model vdw 2.283 3.120 nonbonded pdb=" OG1 THR D 367 " pdb=" OH TYR A 373 " model vdw 2.307 3.040 ... (remaining 80311 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 166 through 424) selection = (chain 'B' and resid 166 through 424) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.580 Find NCS groups from input model: 0.350 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:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.006 0.047 8188 Z= 0.359 Angle : 0.670 8.420 11124 Z= 0.385 Chirality : 0.045 0.176 1320 Planarity : 0.004 0.037 1360 Dihedral : 12.536 81.157 2840 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.24 % Allowed : 0.00 % Favored : 99.76 % 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: 0.47 (0.26), residues: 1028 helix: 0.61 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -0.42 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP B 172 HIS 0.006 0.001 HIS A 306 PHE 0.017 0.002 PHE C 175 TYR 0.015 0.002 TYR B 188 ARG 0.007 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.799 Fit side-chains REVERT: D 187 PHE cc_start: 0.7783 (t80) cc_final: 0.7431 (t80) outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 1.1311 time to fit residues: 172.0499 Evaluate side-chains 117 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.177503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110064 restraints weight = 9311.222| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.44 r_work: 0.3132 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8188 Z= 0.243 Angle : 0.564 7.471 11124 Z= 0.303 Chirality : 0.042 0.140 1320 Planarity : 0.005 0.043 1360 Dihedral : 4.216 23.267 1150 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.78 % Allowed : 11.14 % Favored : 87.09 % 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: 1.08 (0.27), residues: 1028 helix: 1.04 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.25 (0.48), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 172 HIS 0.002 0.001 HIS D 306 PHE 0.014 0.001 PHE A 257 TYR 0.015 0.001 TYR D 188 ARG 0.004 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.807 Fit side-chains REVERT: B 207 VAL cc_start: 0.8396 (t) cc_final: 0.8015 (m) REVERT: B 241 THR cc_start: 0.7630 (m) cc_final: 0.7356 (p) REVERT: D 241 THR cc_start: 0.7613 (m) cc_final: 0.7356 (p) outliers start: 15 outliers final: 4 residues processed: 132 average time/residue: 1.1405 time to fit residues: 160.3324 Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 0.0370 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.179887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123345 restraints weight = 9462.920| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.92 r_work: 0.3188 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8188 Z= 0.192 Angle : 0.517 7.038 11124 Z= 0.276 Chirality : 0.040 0.171 1320 Planarity : 0.005 0.046 1360 Dihedral : 3.901 19.141 1148 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.90 % Allowed : 12.80 % Favored : 85.31 % 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: 1.54 (0.27), residues: 1028 helix: 1.33 (0.18), residues: 816 sheet: None (None), residues: 0 loop : 0.07 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 172 HIS 0.003 0.001 HIS B 306 PHE 0.018 0.001 PHE C 257 TYR 0.015 0.001 TYR D 188 ARG 0.002 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.791 Fit side-chains REVERT: B 241 THR cc_start: 0.8329 (m) cc_final: 0.8101 (p) REVERT: D 241 THR cc_start: 0.8311 (m) cc_final: 0.8102 (p) outliers start: 16 outliers final: 6 residues processed: 140 average time/residue: 1.1894 time to fit residues: 176.4919 Evaluate side-chains 123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 69 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.178232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133988 restraints weight = 9507.986| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.67 r_work: 0.3213 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8188 Z= 0.223 Angle : 0.537 6.733 11124 Z= 0.287 Chirality : 0.041 0.153 1320 Planarity : 0.005 0.045 1360 Dihedral : 3.812 18.087 1148 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.61 % Allowed : 14.45 % Favored : 82.94 % 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: 1.58 (0.26), residues: 1028 helix: 1.40 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.10 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 172 HIS 0.002 0.001 HIS A 179 PHE 0.020 0.001 PHE A 257 TYR 0.015 0.001 TYR D 188 ARG 0.002 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.820 Fit side-chains outliers start: 22 outliers final: 10 residues processed: 137 average time/residue: 1.1212 time to fit residues: 163.3229 Evaluate side-chains 125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.178359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135138 restraints weight = 9416.507| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.68 r_work: 0.3204 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8188 Z= 0.247 Angle : 0.541 6.449 11124 Z= 0.287 Chirality : 0.041 0.127 1320 Planarity : 0.005 0.044 1360 Dihedral : 3.800 17.496 1148 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.20 % Allowed : 15.52 % Favored : 81.28 % 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: 1.67 (0.26), residues: 1028 helix: 1.43 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.07 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 172 HIS 0.002 0.001 HIS B 306 PHE 0.025 0.001 PHE A 257 TYR 0.014 0.001 TYR D 188 ARG 0.002 0.000 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.783 Fit side-chains REVERT: B 308 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7404 (tm-30) REVERT: D 308 GLN cc_start: 0.7644 (tm-30) cc_final: 0.7417 (tm-30) outliers start: 27 outliers final: 13 residues processed: 131 average time/residue: 1.2220 time to fit residues: 169.7480 Evaluate side-chains 125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 0.2980 chunk 61 optimal weight: 0.0070 chunk 64 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130411 restraints weight = 9407.895| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.66 r_work: 0.3232 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8188 Z= 0.192 Angle : 0.522 6.322 11124 Z= 0.275 Chirality : 0.039 0.123 1320 Planarity : 0.005 0.045 1360 Dihedral : 3.706 17.328 1148 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.37 % Allowed : 17.54 % Favored : 80.09 % 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: 1.83 (0.26), residues: 1028 helix: 1.55 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.12 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 172 HIS 0.001 0.000 HIS B 306 PHE 0.028 0.001 PHE A 257 TYR 0.013 0.001 TYR D 188 ARG 0.003 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.825 Fit side-chains REVERT: B 308 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7381 (tm-30) REVERT: D 308 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7402 (tm-30) outliers start: 20 outliers final: 8 residues processed: 137 average time/residue: 1.1626 time to fit residues: 169.2427 Evaluate side-chains 119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 51 optimal weight: 0.0270 chunk 49 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.2238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.182225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131444 restraints weight = 9455.286| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.53 r_work: 0.3302 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8188 Z= 0.154 Angle : 0.516 7.471 11124 Z= 0.269 Chirality : 0.038 0.152 1320 Planarity : 0.004 0.044 1360 Dihedral : 3.594 17.169 1148 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.13 % Allowed : 18.48 % Favored : 79.38 % 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: 2.02 (0.26), residues: 1028 helix: 1.70 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.06 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 172 HIS 0.001 0.000 HIS B 306 PHE 0.031 0.001 PHE A 257 TYR 0.012 0.001 TYR B 188 ARG 0.002 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.823 Fit side-chains REVERT: B 308 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 186 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7619 (t) REVERT: D 308 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7404 (tm-30) outliers start: 18 outliers final: 5 residues processed: 148 average time/residue: 1.1932 time to fit residues: 187.2989 Evaluate side-chains 124 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 18 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: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.182046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 166)---------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125127 restraints weight = 9507.793| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.89 r_work: 0.3235 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8188 Z= 0.184 Angle : 0.540 9.641 11124 Z= 0.280 Chirality : 0.039 0.136 1320 Planarity : 0.005 0.042 1360 Dihedral : 3.550 16.630 1148 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.78 % Allowed : 20.02 % Favored : 78.20 % 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: 2.02 (0.26), residues: 1028 helix: 1.72 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.02 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 172 HIS 0.002 0.000 HIS B 306 PHE 0.038 0.001 PHE A 257 TYR 0.012 0.001 TYR D 188 ARG 0.004 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.840 Fit side-chains REVERT: B 308 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7400 (tm-30) REVERT: D 308 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7379 (tm-30) outliers start: 15 outliers final: 7 residues processed: 129 average time/residue: 1.2158 time to fit residues: 166.8244 Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141932 restraints weight = 9607.944| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.63 r_work: 0.3252 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8188 Z= 0.216 Angle : 0.565 10.329 11124 Z= 0.291 Chirality : 0.040 0.134 1320 Planarity : 0.004 0.039 1360 Dihedral : 3.584 15.768 1148 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.66 % Allowed : 20.73 % Favored : 77.61 % 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: 2.05 (0.26), residues: 1028 helix: 1.74 (0.18), residues: 812 sheet: None (None), residues: 0 loop : 0.07 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 172 HIS 0.002 0.000 HIS B 306 PHE 0.038 0.001 PHE C 257 TYR 0.012 0.001 TYR D 188 ARG 0.003 0.000 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.879 Fit side-chains REVERT: B 308 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7426 (tm-30) REVERT: D 279 MET cc_start: 0.6051 (tmm) cc_final: 0.5776 (tmm) REVERT: D 308 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7396 (tm-30) outliers start: 14 outliers final: 8 residues processed: 129 average time/residue: 1.3611 time to fit residues: 186.4694 Evaluate side-chains 127 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.140070 restraints weight = 9439.392| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.57 r_work: 0.3275 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8188 Z= 0.210 Angle : 0.552 10.354 11124 Z= 0.287 Chirality : 0.040 0.148 1320 Planarity : 0.005 0.039 1360 Dihedral : 3.599 15.824 1148 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.30 % Allowed : 21.68 % Favored : 77.01 % 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: 2.03 (0.26), residues: 1028 helix: 1.73 (0.18), residues: 810 sheet: None (None), residues: 0 loop : 0.06 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 172 HIS 0.002 0.000 HIS B 306 PHE 0.020 0.001 PHE D 409 TYR 0.012 0.001 TYR B 188 ARG 0.005 0.000 ARG C 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: B 308 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7378 (tm-30) REVERT: D 279 MET cc_start: 0.5939 (tmm) cc_final: 0.5661 (tmm) REVERT: D 308 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7385 (tm-30) outliers start: 11 outliers final: 9 residues processed: 125 average time/residue: 1.2971 time to fit residues: 171.5640 Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 79 optimal weight: 0.1980 chunk 37 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.181784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137037 restraints weight = 9492.052| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.61 r_work: 0.3248 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8188 Z= 0.186 Angle : 0.556 10.269 11124 Z= 0.286 Chirality : 0.039 0.145 1320 Planarity : 0.004 0.037 1360 Dihedral : 3.581 15.878 1148 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.30 % Allowed : 21.45 % Favored : 77.25 % 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: 2.09 (0.26), residues: 1028 helix: 1.77 (0.18), residues: 810 sheet: None (None), residues: 0 loop : 0.07 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 172 HIS 0.002 0.000 HIS B 306 PHE 0.037 0.001 PHE A 257 TYR 0.011 0.001 TYR D 188 ARG 0.003 0.000 ARG C 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6396.04 seconds wall clock time: 110 minutes 34.39 seconds (6634.39 seconds total)