Starting phenix.real_space_refine on Sat Aug 23 02:25:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vh0_43230/08_2025/8vh0_43230.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vh0_43230/08_2025/8vh0_43230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vh0_43230/08_2025/8vh0_43230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vh0_43230/08_2025/8vh0_43230.map" model { file = "/net/cci-nas-00/data/ceres_data/8vh0_43230/08_2025/8vh0_43230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vh0_43230/08_2025/8vh0_43230.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.205 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 V 2 8.30 5 S 14 5.16 5 C 5796 2.51 5 N 1522 2.21 5 O 1800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9136 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4559 Classifications: {'peptide': 590} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 552} Chain: "B" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4559 Classifications: {'peptide': 590} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 552} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' CA': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' CA': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.57, per 1000 atoms: 0.28 Number of scatterers: 9136 At special positions: 0 Unit cell: (106.09, 96.82, 98.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 2 22.97 Ca 2 19.99 S 14 16.00 O 1800 8.00 N 1522 7.00 C 5796 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 381.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 12 sheets defined 51.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 38 through 43 removed outlier: 3.997A pdb=" N TYR A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.875A pdb=" N PHE A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.625A pdb=" N ILE A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.725A pdb=" N PHE A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 377 through 402 removed outlier: 3.526A pdb=" N THR A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 426 Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 440 through 459 Processing helix chain 'A' and resid 485 through 502 Processing helix chain 'A' and resid 532 through 550 Processing helix chain 'A' and resid 554 through 578 removed outlier: 3.813A pdb=" N LEU A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.927A pdb=" N TYR B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.744A pdb=" N PHE B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 154 through 170 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 197 through 202 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 240 through 245 removed outlier: 3.629A pdb=" N ILE B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.759A pdb=" N PHE B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 377 through 402 removed outlier: 3.592A pdb=" N THR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 Processing helix chain 'B' and resid 423 through 426 Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'B' and resid 440 through 459 Processing helix chain 'B' and resid 485 through 502 Processing helix chain 'B' and resid 532 through 549 Processing helix chain 'B' and resid 554 through 578 removed outlier: 3.653A pdb=" N LEU B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AA2, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.600A pdb=" N THR A 279 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 279 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.600A pdb=" N THR A 279 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 279 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLN B 282 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 320 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 284 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY B 318 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE B 286 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.750A pdb=" N VAL A 284 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY A 318 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 286 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 370 through 371 Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 508 removed outlier: 4.327A pdb=" N LEU A 530 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 Processing sheet with id=AA8, first strand: chain 'A' and resid 586 through 589 Processing sheet with id=AA9, first strand: chain 'B' and resid 254 through 255 Processing sheet with id=AB1, first strand: chain 'B' and resid 507 through 508 removed outlier: 4.410A pdb=" N LEU B 530 " --> pdb=" O ILE B 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 512 through 514 Processing sheet with id=AB3, first strand: chain 'B' and resid 586 through 589 423 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1639 1.27 - 1.41: 2201 1.41 - 1.54: 5340 1.54 - 1.67: 120 1.67 - 1.80: 24 Bond restraints: 9324 Sorted by residual: bond pdb=" O1 VO4 B 602 " pdb=" V VO4 B 602 " ideal model delta sigma weight residual 1.910 1.550 0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" O1 VO4 A 602 " pdb=" V VO4 A 602 " ideal model delta sigma weight residual 1.910 1.550 0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" O2 VO4 B 602 " pdb=" V VO4 B 602 " ideal model delta sigma weight residual 1.910 1.570 0.340 2.00e-02 2.50e+03 2.90e+02 bond pdb=" O3 VO4 A 602 " pdb=" V VO4 A 602 " ideal model delta sigma weight residual 1.910 1.570 0.340 2.00e-02 2.50e+03 2.89e+02 bond pdb=" O3 VO4 B 602 " pdb=" V VO4 B 602 " ideal model delta sigma weight residual 1.910 1.600 0.310 2.00e-02 2.50e+03 2.41e+02 ... (remaining 9319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 12587 2.94 - 5.87: 80 5.87 - 8.81: 3 8.81 - 11.75: 1 11.75 - 14.68: 3 Bond angle restraints: 12674 Sorted by residual: angle pdb=" CA TYR B 341 " pdb=" C TYR B 341 " pdb=" O TYR B 341 " ideal model delta sigma weight residual 119.41 126.37 -6.96 1.13e+00 7.83e-01 3.80e+01 angle pdb=" O2 VO4 B 602 " pdb=" V VO4 B 602 " pdb=" O3 VO4 B 602 " ideal model delta sigma weight residual 109.47 124.16 -14.68 3.00e+00 1.11e-01 2.40e+01 angle pdb=" C TYR B 341 " pdb=" CA TYR B 341 " pdb=" CB TYR B 341 " ideal model delta sigma weight residual 109.24 117.47 -8.23 1.75e+00 3.27e-01 2.21e+01 angle pdb=" O1 VO4 A 602 " pdb=" V VO4 A 602 " pdb=" O3 VO4 A 602 " ideal model delta sigma weight residual 109.47 123.05 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1 VO4 B 602 " pdb=" V VO4 B 602 " pdb=" O2 VO4 B 602 " ideal model delta sigma weight residual 109.47 122.46 -12.99 3.00e+00 1.11e-01 1.88e+01 ... (remaining 12669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4859 17.94 - 35.87: 542 35.87 - 53.81: 146 53.81 - 71.74: 27 71.74 - 89.68: 18 Dihedral angle restraints: 5592 sinusoidal: 2212 harmonic: 3380 Sorted by residual: dihedral pdb=" CA ALA B 145 " pdb=" C ALA B 145 " pdb=" N MET B 146 " pdb=" CA MET B 146 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" C ILE B 545 " pdb=" N ILE B 545 " pdb=" CA ILE B 545 " pdb=" CB ILE B 545 " ideal model delta harmonic sigma weight residual -122.00 -130.47 8.47 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" CB GLU A 566 " pdb=" CG GLU A 566 " pdb=" CD GLU A 566 " pdb=" OE1 GLU A 566 " ideal model delta sinusoidal sigma weight residual 0.00 89.68 -89.68 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1035 0.043 - 0.085: 280 0.085 - 0.128: 79 0.128 - 0.170: 6 0.170 - 0.213: 4 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CB THR A 412 " pdb=" CA THR A 412 " pdb=" OG1 THR A 412 " pdb=" CG2 THR A 412 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA TYR B 341 " pdb=" N TYR B 341 " pdb=" C TYR B 341 " pdb=" CB TYR B 341 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU B 564 " pdb=" N LEU B 564 " pdb=" C LEU B 564 " pdb=" CB LEU B 564 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 1401 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 341 " 0.022 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C TYR A 341 " -0.080 2.00e-02 2.50e+03 pdb=" O TYR A 341 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU A 342 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 340 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ALA A 340 " -0.075 2.00e-02 2.50e+03 pdb=" O ALA A 340 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR A 341 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 340 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.26e+01 pdb=" C ALA B 340 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA B 340 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR B 341 " -0.021 2.00e-02 2.50e+03 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 857 2.74 - 3.28: 10355 3.28 - 3.82: 19168 3.82 - 4.36: 23516 4.36 - 4.90: 35694 Nonbonded interactions: 89590 Sorted by model distance: nonbonded pdb=" OG1 THR B 412 " pdb=" OH TYR B 554 " model vdw 2.196 3.040 nonbonded pdb=" O LEU A 166 " pdb=" OH TYR A 186 " model vdw 2.199 3.040 nonbonded pdb=" O LEU B 166 " pdb=" OH TYR B 186 " model vdw 2.204 3.040 nonbonded pdb=" N GLY A 138 " pdb=" OE1 GLU A 575 " model vdw 2.209 3.120 nonbonded pdb=" O THR A 330 " pdb=" OG SER B 277 " model vdw 2.214 3.040 ... (remaining 89585 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 12.680 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.560 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:9.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.010 0.360 9326 Z= 0.573 Angle : 0.651 14.684 12674 Z= 0.353 Chirality : 0.043 0.213 1404 Planarity : 0.004 0.046 1704 Dihedral : 17.125 89.678 3416 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 2.37 % Allowed : 19.34 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.24), residues: 1176 helix: 0.74 (0.22), residues: 532 sheet: None (None), residues: 0 loop : 0.56 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 283 TYR 0.030 0.003 TYR A 341 PHE 0.014 0.002 PHE B 479 TRP 0.011 0.002 TRP B 331 HIS 0.006 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00983 ( 9324) covalent geometry : angle 0.65145 (12674) hydrogen bonds : bond 0.13895 ( 417) hydrogen bonds : angle 6.46065 ( 1206) Misc. bond : bond 0.18200 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 LYS cc_start: 0.7914 (tmmt) cc_final: 0.7418 (ttmp) REVERT: B 541 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6994 (t70) outliers start: 23 outliers final: 12 residues processed: 130 average time/residue: 0.5076 time to fit residues: 71.2913 Evaluate side-chains 113 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 557 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN B 85 ASN B 127 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121189 restraints weight = 10259.020| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.29 r_work: 0.3403 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9326 Z= 0.223 Angle : 0.577 5.551 12674 Z= 0.307 Chirality : 0.042 0.144 1404 Planarity : 0.004 0.037 1704 Dihedral : 6.426 73.849 1283 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 4.63 % Allowed : 16.26 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.24), residues: 1176 helix: 0.79 (0.22), residues: 530 sheet: None (None), residues: 0 loop : 0.66 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 283 TYR 0.024 0.003 TYR A 341 PHE 0.018 0.002 PHE B 479 TRP 0.009 0.002 TRP B 331 HIS 0.007 0.002 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 9324) covalent geometry : angle 0.57696 (12674) hydrogen bonds : bond 0.05207 ( 417) hydrogen bonds : angle 5.51015 ( 1206) Misc. bond : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 104 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: A 439 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: A 448 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: B 13 LYS cc_start: 0.7757 (mmtm) cc_final: 0.7408 (tppt) REVERT: B 90 LYS cc_start: 0.7737 (tmmt) cc_final: 0.6846 (ttmp) REVERT: B 173 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7961 (mt) REVERT: B 252 SER cc_start: 0.8008 (OUTLIER) cc_final: 0.7749 (t) REVERT: B 272 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: B 438 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7240 (mm-30) REVERT: B 558 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.6692 (mp10) outliers start: 45 outliers final: 10 residues processed: 140 average time/residue: 0.5412 time to fit residues: 81.7655 Evaluate side-chains 112 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120023 restraints weight = 10214.974| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.30 r_work: 0.3381 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9326 Z= 0.233 Angle : 0.569 5.737 12674 Z= 0.302 Chirality : 0.042 0.143 1404 Planarity : 0.004 0.038 1704 Dihedral : 5.857 74.192 1267 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.47 % Favored : 97.36 % Rotamer: Outliers : 4.42 % Allowed : 17.08 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.24), residues: 1176 helix: 0.69 (0.22), residues: 532 sheet: None (None), residues: 0 loop : 0.57 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 283 TYR 0.026 0.003 TYR A 341 PHE 0.016 0.002 PHE B 479 TRP 0.007 0.002 TRP B 125 HIS 0.007 0.002 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 9324) covalent geometry : angle 0.56923 (12674) hydrogen bonds : bond 0.05074 ( 417) hydrogen bonds : angle 5.41009 ( 1206) Misc. bond : bond 0.00196 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: A 448 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: B 13 LYS cc_start: 0.7791 (mmtm) cc_final: 0.7422 (tppt) REVERT: B 89 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7466 (mt-10) REVERT: B 90 LYS cc_start: 0.7639 (tmmt) cc_final: 0.6710 (ttmp) REVERT: B 173 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8051 (mt) REVERT: B 252 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7726 (t) REVERT: B 272 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: B 438 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7231 (mm-30) REVERT: B 558 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8145 (mm-40) outliers start: 43 outliers final: 10 residues processed: 134 average time/residue: 0.5653 time to fit residues: 81.5481 Evaluate side-chains 107 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 370 GLN B 264 ASN B 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.137032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122472 restraints weight = 10466.094| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.33 r_work: 0.3414 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.004 0.068 9326 Z= 0.177 Angle : 0.533 6.759 12674 Z= 0.282 Chirality : 0.040 0.140 1404 Planarity : 0.004 0.036 1704 Dihedral : 5.717 74.885 1266 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.98 % Favored : 96.85 % Rotamer: Outliers : 4.42 % Allowed : 17.70 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.24), residues: 1176 helix: 0.74 (0.22), residues: 532 sheet: -0.66 (1.38), residues: 18 loop : 0.68 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.028 0.003 TYR B 341 PHE 0.014 0.002 PHE B 479 TRP 0.007 0.002 TRP B 125 HIS 0.006 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9324) covalent geometry : angle 0.53325 (12674) hydrogen bonds : bond 0.04635 ( 417) hydrogen bonds : angle 5.26486 ( 1206) Misc. bond : bond 0.00135 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7456 (ttpt) REVERT: A 172 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: A 182 LYS cc_start: 0.7928 (ptmt) cc_final: 0.7604 (ptpt) REVERT: A 448 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: A 479 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8181 (t80) REVERT: B 13 LYS cc_start: 0.7735 (mmtm) cc_final: 0.7318 (tppt) REVERT: B 89 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7423 (mt-10) REVERT: B 173 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7651 (mt) REVERT: B 252 SER cc_start: 0.7938 (OUTLIER) cc_final: 0.7646 (t) REVERT: B 272 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: B 438 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7113 (mm-30) REVERT: B 558 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8078 (mm-40) REVERT: B 574 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7323 (mt-10) outliers start: 43 outliers final: 11 residues processed: 141 average time/residue: 0.5248 time to fit residues: 80.2975 Evaluate side-chains 115 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122178 restraints weight = 10304.753| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.30 r_work: 0.3406 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9326 Z= 0.196 Angle : 0.541 6.894 12674 Z= 0.285 Chirality : 0.041 0.142 1404 Planarity : 0.004 0.036 1704 Dihedral : 5.711 74.337 1266 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 3.91 % Allowed : 18.52 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.24), residues: 1176 helix: 0.74 (0.22), residues: 532 sheet: -0.60 (1.39), residues: 18 loop : 0.67 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.030 0.003 TYR B 341 PHE 0.016 0.002 PHE B 479 TRP 0.007 0.002 TRP A 331 HIS 0.006 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 9324) covalent geometry : angle 0.54060 (12674) hydrogen bonds : bond 0.04676 ( 417) hydrogen bonds : angle 5.26276 ( 1206) Misc. bond : bond 0.00152 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: A 182 LYS cc_start: 0.7927 (ptmt) cc_final: 0.7643 (ptpt) REVERT: A 356 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7634 (t70) REVERT: A 448 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: A 479 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8146 (t80) REVERT: B 13 LYS cc_start: 0.7821 (mmtm) cc_final: 0.7413 (tppt) REVERT: B 90 LYS cc_start: 0.7650 (tmmt) cc_final: 0.6623 (ttmp) REVERT: B 173 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7781 (mt) REVERT: B 272 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: B 391 ARG cc_start: 0.8458 (mmt-90) cc_final: 0.8228 (mpt-90) REVERT: B 438 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7248 (mm-30) REVERT: B 479 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: B 523 LYS cc_start: 0.7929 (tptm) cc_final: 0.7661 (tppp) REVERT: B 558 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8094 (mm-40) REVERT: B 574 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7512 (mt-10) outliers start: 38 outliers final: 13 residues processed: 133 average time/residue: 0.5068 time to fit residues: 73.1786 Evaluate side-chains 119 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 13 optimal weight: 0.0470 chunk 114 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.139172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124715 restraints weight = 10305.646| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.30 r_work: 0.3441 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9326 Z= 0.156 Angle : 0.511 6.286 12674 Z= 0.270 Chirality : 0.040 0.137 1404 Planarity : 0.004 0.036 1704 Dihedral : 5.622 74.739 1266 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.64 % Favored : 97.19 % Rotamer: Outliers : 3.70 % Allowed : 18.62 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.24), residues: 1176 helix: 0.82 (0.22), residues: 532 sheet: None (None), residues: 0 loop : 0.59 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 391 TYR 0.031 0.002 TYR B 341 PHE 0.014 0.001 PHE B 479 TRP 0.007 0.002 TRP B 125 HIS 0.006 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9324) covalent geometry : angle 0.51076 (12674) hydrogen bonds : bond 0.04402 ( 417) hydrogen bonds : angle 5.15295 ( 1206) Misc. bond : bond 0.00101 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7552 (ttpt) REVERT: A 172 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: A 182 LYS cc_start: 0.7984 (ptmt) cc_final: 0.7628 (ptpt) REVERT: A 356 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7623 (t70) REVERT: A 448 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: A 479 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8191 (t80) REVERT: B 13 LYS cc_start: 0.7750 (mmtm) cc_final: 0.6979 (mtmt) REVERT: B 90 LYS cc_start: 0.7729 (tmmt) cc_final: 0.6618 (ttmp) REVERT: B 252 SER cc_start: 0.7885 (OUTLIER) cc_final: 0.7641 (t) REVERT: B 558 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7992 (mm-40) REVERT: B 574 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7419 (mt-10) outliers start: 36 outliers final: 8 residues processed: 140 average time/residue: 0.5137 time to fit residues: 77.6810 Evaluate side-chains 116 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 114 optimal weight: 0.8980 chunk 100 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.138602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124485 restraints weight = 10393.749| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.28 r_work: 0.3441 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9326 Z= 0.164 Angle : 0.520 6.043 12674 Z= 0.275 Chirality : 0.040 0.138 1404 Planarity : 0.004 0.036 1704 Dihedral : 5.600 73.939 1266 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 3.81 % Allowed : 18.72 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.24), residues: 1176 helix: 0.80 (0.22), residues: 532 sheet: None (None), residues: 0 loop : 0.59 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 391 TYR 0.031 0.003 TYR B 341 PHE 0.016 0.001 PHE B 479 TRP 0.007 0.002 TRP B 125 HIS 0.006 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9324) covalent geometry : angle 0.52013 (12674) hydrogen bonds : bond 0.04424 ( 417) hydrogen bonds : angle 5.15546 ( 1206) Misc. bond : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7611 (ttpt) REVERT: A 172 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8043 (mm-30) REVERT: A 182 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7651 (ptpt) REVERT: A 219 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: A 356 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7613 (t70) REVERT: A 371 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: A 448 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: A 479 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8215 (t80) REVERT: B 13 LYS cc_start: 0.7797 (mmtm) cc_final: 0.7009 (mtmt) REVERT: B 90 LYS cc_start: 0.7650 (tmmt) cc_final: 0.6681 (ttmp) REVERT: B 252 SER cc_start: 0.7881 (OUTLIER) cc_final: 0.7639 (t) REVERT: B 438 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7218 (mm-30) REVERT: B 558 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8017 (mm-40) REVERT: B 574 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7393 (mt-10) outliers start: 37 outliers final: 8 residues processed: 134 average time/residue: 0.4590 time to fit residues: 66.4038 Evaluate side-chains 120 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124288 restraints weight = 10236.293| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.29 r_work: 0.3436 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9326 Z= 0.170 Angle : 0.522 5.925 12674 Z= 0.275 Chirality : 0.040 0.139 1404 Planarity : 0.004 0.037 1704 Dihedral : 5.569 73.249 1266 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.89 % Favored : 96.94 % Rotamer: Outliers : 3.29 % Allowed : 19.14 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.25), residues: 1176 helix: 0.82 (0.22), residues: 530 sheet: -0.74 (1.36), residues: 18 loop : 0.73 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 391 TYR 0.031 0.003 TYR B 341 PHE 0.015 0.001 PHE B 479 TRP 0.006 0.002 TRP B 331 HIS 0.005 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9324) covalent geometry : angle 0.52185 (12674) hydrogen bonds : bond 0.04425 ( 417) hydrogen bonds : angle 5.14787 ( 1206) Misc. bond : bond 0.00128 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: A 219 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8130 (tp30) REVERT: A 356 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7698 (t70) REVERT: A 391 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.8007 (mtt-85) REVERT: A 448 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: A 479 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8179 (t80) REVERT: B 13 LYS cc_start: 0.7803 (mmtm) cc_final: 0.7003 (mtmt) REVERT: B 90 LYS cc_start: 0.7515 (tmmt) cc_final: 0.6609 (ttmp) REVERT: B 252 SER cc_start: 0.7889 (OUTLIER) cc_final: 0.7641 (t) REVERT: B 438 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7205 (mm-30) REVERT: B 558 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8028 (mm-40) outliers start: 32 outliers final: 10 residues processed: 131 average time/residue: 0.4742 time to fit residues: 67.1607 Evaluate side-chains 116 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125388 restraints weight = 10257.115| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.29 r_work: 0.3450 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9326 Z= 0.158 Angle : 0.519 5.710 12674 Z= 0.274 Chirality : 0.040 0.137 1404 Planarity : 0.004 0.037 1704 Dihedral : 5.505 73.065 1266 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.55 % Favored : 97.28 % Rotamer: Outliers : 2.88 % Allowed : 19.24 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.25), residues: 1176 helix: 0.84 (0.22), residues: 530 sheet: -0.84 (1.35), residues: 18 loop : 0.73 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 391 TYR 0.029 0.002 TYR B 341 PHE 0.015 0.001 PHE B 479 TRP 0.007 0.002 TRP B 125 HIS 0.005 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9324) covalent geometry : angle 0.51912 (12674) hydrogen bonds : bond 0.04334 ( 417) hydrogen bonds : angle 5.12819 ( 1206) Misc. bond : bond 0.00116 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7239 (mt-10) REVERT: A 90 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.6916 (ttmt) REVERT: A 167 MET cc_start: 0.8706 (mtt) cc_final: 0.8459 (mtt) REVERT: A 172 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: A 356 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7701 (t70) REVERT: A 442 ASP cc_start: 0.6594 (m-30) cc_final: 0.6123 (t0) REVERT: A 448 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: A 479 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8209 (t80) REVERT: B 13 LYS cc_start: 0.7758 (mmtm) cc_final: 0.6984 (mtmt) REVERT: B 90 LYS cc_start: 0.7497 (tmmt) cc_final: 0.6595 (ttmp) REVERT: B 252 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7624 (t) REVERT: B 558 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7999 (mm-40) REVERT: B 574 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7237 (mt-10) outliers start: 28 outliers final: 10 residues processed: 129 average time/residue: 0.4390 time to fit residues: 61.0464 Evaluate side-chains 121 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 34 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 72 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127246 restraints weight = 10305.682| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.27 r_work: 0.3480 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9326 Z= 0.143 Angle : 0.510 5.378 12674 Z= 0.269 Chirality : 0.039 0.136 1404 Planarity : 0.004 0.037 1704 Dihedral : 5.129 72.862 1263 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.55 % Favored : 97.28 % Rotamer: Outliers : 2.16 % Allowed : 19.96 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.24), residues: 1176 helix: 0.88 (0.22), residues: 532 sheet: -0.85 (1.35), residues: 18 loop : 0.69 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 391 TYR 0.028 0.002 TYR B 341 PHE 0.018 0.001 PHE B 479 TRP 0.007 0.002 TRP B 125 HIS 0.005 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9324) covalent geometry : angle 0.51038 (12674) hydrogen bonds : bond 0.04190 ( 417) hydrogen bonds : angle 5.08272 ( 1206) Misc. bond : bond 0.00107 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7215 (tm-30) REVERT: A 90 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.6941 (ttmt) REVERT: A 172 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7989 (mm-30) REVERT: A 356 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7684 (t70) REVERT: A 442 ASP cc_start: 0.6498 (m-30) cc_final: 0.6058 (t0) REVERT: A 448 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: B 13 LYS cc_start: 0.7741 (mmtm) cc_final: 0.6982 (mtmt) REVERT: B 90 LYS cc_start: 0.7511 (tmmt) cc_final: 0.6661 (ttmp) REVERT: B 252 SER cc_start: 0.7842 (OUTLIER) cc_final: 0.7607 (t) REVERT: B 558 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7963 (mm-40) REVERT: B 574 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7128 (mt-10) outliers start: 21 outliers final: 7 residues processed: 125 average time/residue: 0.5110 time to fit residues: 68.9930 Evaluate side-chains 117 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123409 restraints weight = 10172.828| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.27 r_work: 0.3430 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 9326 Z= 0.201 Angle : 0.556 6.401 12674 Z= 0.291 Chirality : 0.041 0.143 1404 Planarity : 0.004 0.046 1704 Dihedral : 5.213 70.949 1263 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.89 % Favored : 96.94 % Rotamer: Outliers : 2.26 % Allowed : 20.06 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.24), residues: 1176 helix: 0.82 (0.22), residues: 530 sheet: -0.70 (1.37), residues: 18 loop : 0.72 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 391 TYR 0.030 0.003 TYR B 341 PHE 0.022 0.002 PHE B 479 TRP 0.007 0.002 TRP B 331 HIS 0.005 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 9324) covalent geometry : angle 0.55553 (12674) hydrogen bonds : bond 0.04561 ( 417) hydrogen bonds : angle 5.19024 ( 1206) Misc. bond : bond 0.00167 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.81 seconds wall clock time: 59 minutes 57.44 seconds (3597.44 seconds total)