Starting phenix.real_space_refine on Wed Feb 12 13:53:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukc_26576/02_2025/7ukc_26576.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukc_26576/02_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_26576/02_2025/7ukc_26576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukc_26576/02_2025/7ukc_26576.map" model { file = "/net/cci-nas-00/data/ceres_data/7ukc_26576/02_2025/7ukc_26576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukc_26576/02_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-5592/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: 6.18, per 1000 atoms: 0.77 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: 1.92 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: 0.73 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: 2.26 Time building geometry restraints manager: 2.24 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: 2.130 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: 0.060 Set scattering table: 0.090 Process input model: 22.070 Find NCS groups from input model: 0.330 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- 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 : 0.950 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: 1.1765 time to fit residues: 178.7406 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 : 0.884 ------------------------------------------------------------------------------- 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 = 9311.216| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.44 r_work: 0.3132 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 0.704 Fit side-chains REVERT: B 207 VAL cc_start: 0.8394 (t) cc_final: 0.8014 (m) REVERT: B 241 THR cc_start: 0.7622 (m) cc_final: 0.7348 (p) REVERT: D 241 THR cc_start: 0.7607 (m) cc_final: 0.7350 (p) outliers start: 15 outliers final: 4 residues processed: 132 average time/residue: 1.1791 time to fit residues: 166.4977 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 : 0.964 ------------------------------------------------------------------------------- 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: 0.6980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 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: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.178376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 131)---------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119197 restraints weight = 9522.943| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.94 r_work: 0.3173 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8188 Z= 0.212 Angle : 0.521 6.950 11124 Z= 0.278 Chirality : 0.040 0.177 1320 Planarity : 0.005 0.045 1360 Dihedral : 3.901 18.668 1148 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.13 % Allowed : 12.80 % Favored : 85.07 % 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 : 0.08 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 172 HIS 0.002 0.001 HIS B 306 PHE 0.018 0.001 PHE C 257 TYR 0.015 0.001 TYR D 188 ARG 0.003 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 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.968 Fit side-chains REVERT: B 241 THR cc_start: 0.8366 (m) cc_final: 0.8136 (p) REVERT: D 241 THR cc_start: 0.8329 (m) cc_final: 0.8116 (p) outliers start: 18 outliers final: 8 residues processed: 146 average time/residue: 1.2407 time to fit residues: 191.8275 Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 263 SER 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: 0.9980 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 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: 0.7582 ------------------------------------------------------------------------------- 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 = 0.178072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133012 restraints weight = 9508.632| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.62 r_work: 0.3203 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1668 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= 0.224 Angle : 0.537 6.651 11124 Z= 0.287 Chirality : 0.040 0.147 1320 Planarity : 0.005 0.044 1360 Dihedral : 3.807 18.010 1148 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.37 % Allowed : 14.81 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.59 (0.26), residues: 1028 helix: 1.40 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.08 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 172 HIS 0.002 0.001 HIS A 179 PHE 0.020 0.001 PHE A 257 TYR 0.014 0.001 TYR D 188 ARG 0.002 0.000 ARG A 293 *********************** 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 140 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.851 Fit side-chains REVERT: B 308 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7367 (tm-30) REVERT: D 308 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7407 (tm-30) outliers start: 20 outliers final: 9 residues processed: 129 average time/residue: 1.2881 time to fit residues: 175.8774 Evaluate side-chains 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 275 ILE 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 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: 0.7980 chunk 23 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.179701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133273 restraints weight = 9435.889| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.59 r_work: 0.3238 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1849 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= 0.204 Angle : 0.525 6.968 11124 Z= 0.278 Chirality : 0.040 0.124 1320 Planarity : 0.005 0.044 1360 Dihedral : 3.741 17.439 1148 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.61 % Allowed : 16.47 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.75 (0.26), residues: 1028 helix: 1.51 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.04 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 172 HIS 0.001 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 140 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.843 Fit side-chains REVERT: B 308 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7328 (tm-30) REVERT: D 308 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7330 (tm-30) outliers start: 22 outliers final: 10 residues processed: 131 average time/residue: 1.2622 time to fit residues: 174.8307 Evaluate side-chains 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL 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 323 GLU 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: 0.9990 chunk 61 optimal weight: 0.0070 chunk 64 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 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 = 0.4042 r_free = 0.4042 target = 0.179312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 161)---------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122021 restraints weight = 9450.802| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.81 r_work: 0.3175 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8188 Z= 0.193 Angle : 0.525 6.480 11124 Z= 0.276 Chirality : 0.039 0.123 1320 Planarity : 0.005 0.042 1360 Dihedral : 3.704 17.284 1148 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.13 % Allowed : 18.25 % Favored : 79.62 % 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: 1.85 (0.26), residues: 1028 helix: 1.58 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.01 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 172 HIS 0.001 0.000 HIS B 306 PHE 0.027 0.001 PHE A 257 TYR 0.013 0.001 TYR D 188 ARG 0.002 0.000 ARG B 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 137 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.873 Fit side-chains REVERT: B 308 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7323 (tm-30) REVERT: D 308 GLN cc_start: 0.7608 (tm-30) cc_final: 0.7309 (tm-30) outliers start: 18 outliers final: 6 residues processed: 131 average time/residue: 1.2449 time to fit residues: 172.9302 Evaluate side-chains 119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 36 optimal weight: 0.0970 chunk 14 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 68 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.181114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137201 restraints weight = 9435.035| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.60 r_work: 0.3318 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2174 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= 0.166 Angle : 0.511 7.805 11124 Z= 0.267 Chirality : 0.038 0.153 1320 Planarity : 0.004 0.042 1360 Dihedral : 3.591 16.947 1148 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.25 % Allowed : 18.84 % Favored : 78.91 % 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: 2.00 (0.26), residues: 1028 helix: 1.68 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.08 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 172 HIS 0.001 0.000 HIS D 306 PHE 0.030 0.001 PHE A 257 TYR 0.012 0.001 TYR B 188 ARG 0.003 0.000 ARG D 247 *********************** 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 152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.926 Fit side-chains REVERT: B 308 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7397 (tm-30) REVERT: D 308 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7401 (tm-30) outliers start: 19 outliers final: 8 residues processed: 146 average time/residue: 1.2451 time to fit residues: 193.6828 Evaluate side-chains 130 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 43 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.179485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132056 restraints weight = 9494.650| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.57 r_work: 0.3246 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8188 Z= 0.245 Angle : 0.573 9.337 11124 Z= 0.297 Chirality : 0.040 0.142 1320 Planarity : 0.005 0.039 1360 Dihedral : 3.632 16.561 1148 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.01 % Allowed : 20.02 % Favored : 77.96 % 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: 1.87 (0.26), residues: 1028 helix: 1.61 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -0.06 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 172 HIS 0.002 0.001 HIS B 306 PHE 0.039 0.001 PHE A 257 TYR 0.012 0.001 TYR D 188 ARG 0.003 0.000 ARG C 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 137 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.938 Fit side-chains REVERT: B 308 GLN cc_start: 0.7665 (tm-30) cc_final: 0.7354 (tm-30) REVERT: D 308 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7364 (tm-30) outliers start: 17 outliers final: 11 residues processed: 132 average time/residue: 1.2273 time to fit residues: 171.8056 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 : 0.894 ------------------------------------------------------------------------------- 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 415 GLN Chi-restraints excluded: chain C residue 186 VAL 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 290 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.0070 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 0.1980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.180550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135817 restraints weight = 9578.929| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.55 r_work: 0.3295 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2259 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= 0.189 Angle : 0.563 10.380 11124 Z= 0.287 Chirality : 0.039 0.139 1320 Planarity : 0.004 0.039 1360 Dihedral : 3.600 16.286 1148 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.18 % Allowed : 21.80 % 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: 2.06 (0.26), residues: 1028 helix: 1.73 (0.18), residues: 812 sheet: None (None), residues: 0 loop : 0.15 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 172 HIS 0.002 0.000 HIS B 306 PHE 0.041 0.001 PHE C 257 TYR 0.012 0.001 TYR D 188 ARG 0.003 0.000 ARG A 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 125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.846 Fit side-chains REVERT: B 308 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7369 (tm-30) REVERT: D 308 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7374 (tm-30) outliers start: 10 outliers final: 8 residues processed: 122 average time/residue: 1.2483 time to fit residues: 161.5128 Evaluate side-chains 122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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: 0.5980 chunk 77 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.179994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135196 restraints weight = 9426.516| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.54 r_work: 0.3275 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 0.046 8188 Z= 0.207 Angle : 0.563 10.458 11124 Z= 0.290 Chirality : 0.039 0.133 1320 Planarity : 0.004 0.038 1360 Dihedral : 3.601 15.945 1148 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.30 % Allowed : 21.92 % Favored : 76.78 % 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: 2.05 (0.26), residues: 1028 helix: 1.73 (0.18), residues: 810 sheet: None (None), residues: 0 loop : 0.10 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 172 HIS 0.002 0.000 HIS D 306 PHE 0.045 0.001 PHE C 257 TYR 0.012 0.001 TYR D 188 ARG 0.002 0.000 ARG A 296 ********************** 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 130 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.701 Fit side-chains REVERT: B 308 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7434 (tm-30) REVERT: C 275 ILE cc_start: 0.8676 (mp) cc_final: 0.8460 (mp) REVERT: D 308 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7397 (tm-30) outliers start: 11 outliers final: 9 residues processed: 127 average time/residue: 1.1974 time to fit residues: 161.3440 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 : 0.931 ------------------------------------------------------------------------------- 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: 9.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.180479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135055 restraints weight = 9482.086| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.49 r_work: 0.3298 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8188 Z= 0.200 Angle : 0.570 10.282 11124 Z= 0.292 Chirality : 0.039 0.151 1320 Planarity : 0.005 0.037 1360 Dihedral : 3.604 15.834 1148 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.42 % Allowed : 21.80 % Favored : 76.78 % 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: 2.09 (0.26), residues: 1028 helix: 1.76 (0.18), residues: 810 sheet: None (None), residues: 0 loop : 0.12 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 172 HIS 0.002 0.000 HIS D 306 PHE 0.049 0.001 PHE C 257 TYR 0.012 0.001 TYR B 188 ARG 0.003 0.000 ARG C 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6489.13 seconds wall clock time: 115 minutes 23.13 seconds (6923.13 seconds total)