Starting phenix.real_space_refine on Wed Sep 17 14:40:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjq_43291/09_2025/8vjq_43291.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjq_43291/09_2025/8vjq_43291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vjq_43291/09_2025/8vjq_43291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjq_43291/09_2025/8vjq_43291.map" model { file = "/net/cci-nas-00/data/ceres_data/8vjq_43291/09_2025/8vjq_43291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjq_43291/09_2025/8vjq_43291.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 V 2 8.30 5 Br 2 7.06 5 S 14 5.16 5 C 5796 2.51 5 N 1522 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9132 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4558 Classifications: {'peptide': 590} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 552} Chain: "B" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4558 Classifications: {'peptide': 590} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 552} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' BR': 1, ' CA': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' BR': 1, ' CA': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.44, per 1000 atoms: 0.27 Number of scatterers: 9132 At special positions: 0 Unit cell: (106.496, 93.184, 100.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 2 34.99 V 2 22.97 Ca 2 19.99 S 14 16.00 O 1794 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: 1.01 Conformation dependent library (CDL) restraints added in 366.8 milliseconds Enol-peptide restraints added in 476.8 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: 47 helices and 13 sheets defined 49.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.131A pdb=" N TYR A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.082A 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 119 Processing helix chain 'A' and resid 128 through 133 removed outlier: 4.112A pdb=" N GLY A 131 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 removed outlier: 3.504A pdb=" N VAL A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 4.447A pdb=" N GLU A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) 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: 3.577A pdb=" N ILE A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 4.216A pdb=" N PHE A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.942A 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 removed outlier: 3.525A pdb=" N ASP A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 402 removed outlier: 4.293A pdb=" N ALA A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 423 through 426 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 removed outlier: 3.648A pdb=" N ARG A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 578 removed outlier: 3.885A 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: 3.988A pdb=" N TYR B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.695A pdb=" N ALA B 79 " --> pdb=" O ASP B 75 " (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 154 through 170 removed outlier: 3.520A pdb=" N VAL B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 183 through 197 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 Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 338 through 352 Processing helix chain 'B' and resid 377 through 402 removed outlier: 4.246A pdb=" N THR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 426 Proline residue: B 423 - end of helix 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 458 Processing helix chain 'B' and resid 485 through 502 Processing helix chain 'B' and resid 532 through 550 Processing helix chain 'B' and resid 554 through 580 removed outlier: 3.759A pdb=" N LEU B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 580 " --> pdb=" O GLN B 576 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 5.560A pdb=" N TRP A 125 " --> pdb=" O ASP B 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.741A pdb=" N THR A 279 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 279 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.741A pdb=" N THR A 279 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 279 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 286 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY B 318 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 7.136A pdb=" N VAL A 284 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLY A 318 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 286 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 370 through 371 Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 508 removed outlier: 4.638A pdb=" N LEU A 530 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 514 Processing sheet with id=AA9, first strand: chain 'A' and resid 586 through 589 Processing sheet with id=AB1, first strand: chain 'B' and resid 254 through 255 Processing sheet with id=AB2, first strand: chain 'B' and resid 507 through 508 removed outlier: 4.700A pdb=" N LEU B 530 " --> pdb=" O ILE B 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 512 through 514 Processing sheet with id=AB4, first strand: chain 'B' and resid 586 through 589 414 hydrogen bonds defined for protein. 1200 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: 1.48 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1648 1.31 - 1.43: 2326 1.43 - 1.56: 5318 1.56 - 1.68: 6 1.68 - 1.80: 24 Bond restraints: 9322 Sorted by residual: bond pdb=" O1 VO4 B 603 " pdb=" V VO4 B 603 " ideal model delta sigma weight residual 1.910 1.549 0.361 2.00e-02 2.50e+03 3.25e+02 bond pdb=" O1 VO4 A 603 " pdb=" V VO4 A 603 " 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 603 " pdb=" V VO4 B 603 " ideal model delta sigma weight residual 1.910 1.571 0.339 2.00e-02 2.50e+03 2.87e+02 bond pdb=" O2 VO4 A 603 " pdb=" V VO4 A 603 " ideal model delta sigma weight residual 1.910 1.573 0.337 2.00e-02 2.50e+03 2.84e+02 bond pdb=" O3 VO4 B 603 " pdb=" V VO4 B 603 " ideal model delta sigma weight residual 1.910 1.599 0.311 2.00e-02 2.50e+03 2.42e+02 ... (remaining 9317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 12605 3.92 - 7.83: 50 7.83 - 11.75: 9 11.75 - 15.66: 4 15.66 - 19.58: 2 Bond angle restraints: 12670 Sorted by residual: angle pdb=" CA ASP B 335 " pdb=" CB ASP B 335 " pdb=" CG ASP B 335 " ideal model delta sigma weight residual 112.60 129.29 -16.69 1.00e+00 1.00e+00 2.79e+02 angle pdb=" CA ASP A 335 " pdb=" CB ASP A 335 " pdb=" CG ASP A 335 " ideal model delta sigma weight residual 112.60 121.89 -9.29 1.00e+00 1.00e+00 8.64e+01 angle pdb=" CA PRO B 33 " pdb=" N PRO B 33 " pdb=" CD PRO B 33 " ideal model delta sigma weight residual 112.00 100.88 11.12 1.40e+00 5.10e-01 6.31e+01 angle pdb=" C ARG B 397 " pdb=" N TYR B 398 " pdb=" CA TYR B 398 " ideal model delta sigma weight residual 120.54 110.53 10.01 1.35e+00 5.49e-01 5.50e+01 angle pdb=" O ARG B 397 " pdb=" C ARG B 397 " pdb=" N TYR B 398 " ideal model delta sigma weight residual 122.23 131.45 -9.22 1.30e+00 5.92e-01 5.03e+01 ... (remaining 12665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4796 17.80 - 35.61: 604 35.61 - 53.41: 142 53.41 - 71.22: 38 71.22 - 89.02: 10 Dihedral angle restraints: 5590 sinusoidal: 2210 harmonic: 3380 Sorted by residual: dihedral pdb=" C HIS B 487 " pdb=" N HIS B 487 " pdb=" CA HIS B 487 " pdb=" CB HIS B 487 " ideal model delta harmonic sigma weight residual -122.60 -109.28 -13.32 0 2.50e+00 1.60e-01 2.84e+01 dihedral pdb=" C ARG A 397 " pdb=" N ARG A 397 " pdb=" CA ARG A 397 " pdb=" CB ARG A 397 " ideal model delta harmonic sigma weight residual -122.60 -112.84 -9.76 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" CA LEU B 337 " pdb=" C LEU B 337 " pdb=" N TYR B 338 " pdb=" CA TYR B 338 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1126 0.050 - 0.100: 239 0.100 - 0.151: 34 0.151 - 0.201: 1 0.201 - 0.251: 4 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CB THR A 96 " pdb=" CA THR A 96 " pdb=" OG1 THR A 96 " pdb=" CG2 THR A 96 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ASP A 335 " pdb=" N ASP A 335 " pdb=" C ASP A 335 " pdb=" CB ASP A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ARG A 397 " pdb=" N ARG A 397 " pdb=" C ARG A 397 " pdb=" CB ARG A 397 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1401 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 32 " 0.090 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO B 33 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO B 33 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 33 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 288 " -0.076 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO A 289 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 334 " 0.022 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C PHE A 334 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE A 334 " 0.027 2.00e-02 2.50e+03 pdb=" N ASP A 335 " 0.026 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 917 2.74 - 3.28: 10181 3.28 - 3.82: 17699 3.82 - 4.36: 22248 4.36 - 4.90: 36209 Nonbonded interactions: 87254 Sorted by model distance: nonbonded pdb=" NH1 ARG A 408 " pdb=" O VAL A 552 " model vdw 2.198 3.120 nonbonded pdb=" NH2 ARG A 29 " pdb=" OE2 GLU A 575 " model vdw 2.222 3.120 nonbonded pdb=" CE2 TYR A 341 " pdb=" O HOH A 701 " model vdw 2.224 3.340 nonbonded pdb=" NH1 ARG A 406 " pdb=" OD1 ASP A 557 " model vdw 2.226 3.120 nonbonded pdb=" NH2 ARG B 29 " pdb=" OE2 GLU B 575 " model vdw 2.226 3.120 ... (remaining 87249 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: 0.02 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: 10.970 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.500 Find NCS groups from input model: 0.150 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.011 0.361 9324 Z= 0.621 Angle : 0.811 19.579 12670 Z= 0.475 Chirality : 0.043 0.251 1404 Planarity : 0.009 0.128 1702 Dihedral : 17.114 89.022 3414 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.31 % Allowed : 23.87 % Favored : 75.82 % Cbeta Deviations : 0.09 % 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: -0.02 (0.24), residues: 1176 helix: 0.43 (0.22), residues: 528 sheet: -1.41 (1.35), residues: 18 loop : -0.25 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 397 TYR 0.048 0.003 TYR B 341 PHE 0.016 0.001 PHE A 376 TRP 0.009 0.002 TRP B 110 HIS 0.021 0.002 HIS B 487 Details of bonding type rmsd covalent geometry : bond 0.01009 ( 9322) covalent geometry : angle 0.81092 (12670) hydrogen bonds : bond 0.14363 ( 408) hydrogen bonds : angle 7.04827 ( 1200) Misc. bond : bond 0.23318 ( 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 118 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.390 Fit side-chains REVERT: B 515 ASP cc_start: 0.7847 (t0) cc_final: 0.7531 (m-30) REVERT: B 592 ASP cc_start: 0.8285 (p0) cc_final: 0.8037 (p0) outliers start: 3 outliers final: 1 residues processed: 116 average time/residue: 0.1079 time to fit residues: 17.7761 Evaluate side-chains 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 304 GLN A 419 ASN A 542 ASN B 68 ASN B 183 ASN B 224 ASN B 351 ASN B 419 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.140114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.125553 restraints weight = 8933.196| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.18 r_work: 0.3113 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9324 Z= 0.190 Angle : 0.582 6.639 12670 Z= 0.299 Chirality : 0.042 0.171 1404 Planarity : 0.006 0.068 1702 Dihedral : 4.425 41.128 1262 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.91 % Allowed : 21.09 % Favored : 75.00 % 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: 0.43 (0.24), residues: 1176 helix: 0.89 (0.22), residues: 518 sheet: -1.89 (1.18), residues: 18 loop : -0.05 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 405 TYR 0.034 0.003 TYR B 341 PHE 0.015 0.002 PHE A 479 TRP 0.012 0.002 TRP B 199 HIS 0.008 0.002 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9322) covalent geometry : angle 0.58196 (12670) hydrogen bonds : bond 0.04372 ( 408) hydrogen bonds : angle 5.65889 ( 1200) Misc. bond : bond 0.00160 ( 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 173 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.344 Fit side-chains REVERT: A 63 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8356 (mt) REVERT: A 121 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8173 (mm-30) REVERT: A 243 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8503 (tt) REVERT: A 364 GLU cc_start: 0.7520 (tp30) cc_final: 0.6829 (tt0) REVERT: A 501 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7838 (t80) REVERT: B 173 ILE cc_start: 0.8495 (mm) cc_final: 0.8032 (mm) REVERT: B 183 ASN cc_start: 0.7009 (m-40) cc_final: 0.6565 (m110) REVERT: B 438 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6845 (mt-10) REVERT: B 592 ASP cc_start: 0.8290 (p0) cc_final: 0.8029 (p0) outliers start: 38 outliers final: 20 residues processed: 160 average time/residue: 0.1037 time to fit residues: 23.4697 Evaluate side-chains 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 471 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 0.0060 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN B 224 ASN ** B 362 GLN ** 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 = 0.3477 r_free = 0.3477 target = 0.141059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.126764 restraints weight = 8865.429| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.17 r_work: 0.3158 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9324 Z= 0.160 Angle : 0.547 6.230 12670 Z= 0.278 Chirality : 0.040 0.176 1404 Planarity : 0.005 0.053 1702 Dihedral : 4.330 42.223 1262 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.91 % Allowed : 21.71 % Favored : 74.38 % 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: 0.62 (0.24), residues: 1176 helix: 1.02 (0.22), residues: 520 sheet: -1.91 (1.09), residues: 18 loop : 0.07 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 320 TYR 0.031 0.003 TYR B 341 PHE 0.013 0.001 PHE A 479 TRP 0.008 0.001 TRP B 331 HIS 0.007 0.002 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9322) covalent geometry : angle 0.54709 (12670) hydrogen bonds : bond 0.04063 ( 408) hydrogen bonds : angle 5.36895 ( 1200) Misc. bond : bond 0.00049 ( 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 161 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.352 Fit side-chains REVERT: A 121 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8089 (tp30) REVERT: A 243 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8477 (tt) REVERT: A 364 GLU cc_start: 0.7587 (tp30) cc_final: 0.6908 (tt0) REVERT: A 566 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: B 173 ILE cc_start: 0.8384 (mm) cc_final: 0.7886 (mm) REVERT: B 183 ASN cc_start: 0.7057 (m-40) cc_final: 0.6327 (m110) REVERT: B 297 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.6959 (mt) REVERT: B 438 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6869 (mt-10) REVERT: B 592 ASP cc_start: 0.8136 (p0) cc_final: 0.7855 (p0) outliers start: 38 outliers final: 22 residues processed: 150 average time/residue: 0.0945 time to fit residues: 20.3933 Evaluate side-chains 136 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 471 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN A 264 ASN B 224 ASN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.140001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.124062 restraints weight = 8999.453| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.34 r_work: 0.3461 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9324 Z= 0.186 Angle : 0.559 6.415 12670 Z= 0.282 Chirality : 0.041 0.148 1404 Planarity : 0.005 0.054 1702 Dihedral : 4.327 42.514 1262 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.14 % Allowed : 20.68 % Favored : 74.18 % 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: 0.63 (0.24), residues: 1176 helix: 0.99 (0.22), residues: 520 sheet: -2.23 (0.98), residues: 18 loop : 0.13 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.032 0.003 TYR B 341 PHE 0.013 0.001 PHE A 479 TRP 0.009 0.001 TRP B 199 HIS 0.006 0.002 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 9322) covalent geometry : angle 0.55939 (12670) hydrogen bonds : bond 0.04122 ( 408) hydrogen bonds : angle 5.33703 ( 1200) Misc. bond : bond 0.00049 ( 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 174 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 0.358 Fit side-chains REVERT: A 63 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8357 (mt) REVERT: A 68 ASN cc_start: 0.8460 (m110) cc_final: 0.8138 (m-40) REVERT: A 121 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8157 (tp30) REVERT: A 243 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8509 (tt) REVERT: A 364 GLU cc_start: 0.7639 (tp30) cc_final: 0.6892 (tt0) REVERT: A 501 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7933 (t80) REVERT: A 566 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: B 173 ILE cc_start: 0.8474 (mm) cc_final: 0.7930 (mm) REVERT: B 183 ASN cc_start: 0.7092 (m-40) cc_final: 0.6348 (m110) REVERT: B 254 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8314 (t) REVERT: B 297 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.6978 (mt) REVERT: B 438 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6759 (mt-10) REVERT: B 592 ASP cc_start: 0.8178 (p0) cc_final: 0.7922 (p0) outliers start: 50 outliers final: 31 residues processed: 162 average time/residue: 0.0934 time to fit residues: 22.0459 Evaluate side-chains 150 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 485 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 116 optimal weight: 0.3980 chunk 99 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN B 127 ASN B 224 ASN B 358 ASN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.141024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.125218 restraints weight = 8979.484| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.34 r_work: 0.3145 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9324 Z= 0.163 Angle : 0.550 8.419 12670 Z= 0.277 Chirality : 0.040 0.145 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.321 43.145 1262 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.04 % Allowed : 20.78 % Favored : 74.18 % 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: 0.67 (0.24), residues: 1176 helix: 1.06 (0.22), residues: 520 sheet: -2.51 (0.92), residues: 18 loop : 0.14 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.030 0.003 TYR B 341 PHE 0.011 0.001 PHE B 501 TRP 0.008 0.001 TRP B 331 HIS 0.006 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9322) covalent geometry : angle 0.55042 (12670) hydrogen bonds : bond 0.04004 ( 408) hydrogen bonds : angle 5.24049 ( 1200) Misc. bond : bond 0.00051 ( 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 166 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 0.356 Fit side-chains REVERT: A 63 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8375 (mt) REVERT: A 68 ASN cc_start: 0.8553 (m110) cc_final: 0.8112 (m-40) REVERT: A 121 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8141 (tp30) REVERT: A 243 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8484 (tt) REVERT: A 364 GLU cc_start: 0.7631 (tp30) cc_final: 0.6915 (tt0) REVERT: A 471 MET cc_start: 0.8241 (mtp) cc_final: 0.7842 (mtp) REVERT: A 501 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7974 (t80) REVERT: A 566 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: B 173 ILE cc_start: 0.8465 (mm) cc_final: 0.7912 (mm) REVERT: B 183 ASN cc_start: 0.7000 (m-40) cc_final: 0.6272 (m110) REVERT: B 254 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8345 (t) REVERT: B 297 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.6971 (mt) REVERT: B 438 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6851 (mt-10) REVERT: B 501 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: B 515 ASP cc_start: 0.8285 (t0) cc_final: 0.7948 (m-30) REVERT: B 592 ASP cc_start: 0.8012 (p0) cc_final: 0.7715 (p0) outliers start: 49 outliers final: 35 residues processed: 157 average time/residue: 0.0880 time to fit residues: 20.5885 Evaluate side-chains 154 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 535 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.139374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.123258 restraints weight = 8941.524| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.35 r_work: 0.3459 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9324 Z= 0.184 Angle : 0.559 7.567 12670 Z= 0.282 Chirality : 0.041 0.178 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.333 43.396 1262 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.94 % Allowed : 21.50 % Favored : 73.56 % 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: 0.62 (0.24), residues: 1176 helix: 1.00 (0.22), residues: 520 sheet: -2.56 (0.91), residues: 18 loop : 0.11 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.031 0.003 TYR B 341 PHE 0.012 0.001 PHE A 479 TRP 0.009 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9322) covalent geometry : angle 0.55910 (12670) hydrogen bonds : bond 0.04075 ( 408) hydrogen bonds : angle 5.25596 ( 1200) Misc. bond : bond 0.00068 ( 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 162 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 114 time to evaluate : 0.357 Fit side-chains REVERT: A 63 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8364 (mt) REVERT: A 68 ASN cc_start: 0.8534 (m110) cc_final: 0.8137 (m-40) REVERT: A 121 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8153 (tp30) REVERT: A 243 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8511 (tt) REVERT: A 501 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7975 (t80) REVERT: A 566 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: B 173 ILE cc_start: 0.8551 (mm) cc_final: 0.7964 (mm) REVERT: B 183 ASN cc_start: 0.7158 (m-40) cc_final: 0.6240 (m110) REVERT: B 254 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8358 (t) REVERT: B 270 ASP cc_start: 0.7243 (t0) cc_final: 0.7026 (t0) REVERT: B 297 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.6960 (mt) REVERT: B 438 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6792 (mt-10) REVERT: B 501 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: B 515 ASP cc_start: 0.8272 (t0) cc_final: 0.7931 (m-30) REVERT: B 592 ASP cc_start: 0.8055 (p0) cc_final: 0.7777 (p0) outliers start: 48 outliers final: 33 residues processed: 156 average time/residue: 0.0884 time to fit residues: 20.5329 Evaluate side-chains 152 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 501 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN B 224 ASN B 362 GLN B 370 GLN B 402 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.139323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.123228 restraints weight = 8978.497| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.36 r_work: 0.3134 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9324 Z= 0.176 Angle : 0.560 7.209 12670 Z= 0.282 Chirality : 0.041 0.161 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.346 43.824 1262 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.94 % Allowed : 21.60 % Favored : 73.46 % 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: 0.70 (0.24), residues: 1176 helix: 1.04 (0.22), residues: 512 sheet: -2.61 (0.88), residues: 18 loop : 0.20 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.031 0.003 TYR B 341 PHE 0.011 0.001 PHE B 501 TRP 0.009 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9322) covalent geometry : angle 0.55963 (12670) hydrogen bonds : bond 0.04034 ( 408) hydrogen bonds : angle 5.23841 ( 1200) Misc. bond : bond 0.00050 ( 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 164 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 116 time to evaluate : 0.409 Fit side-chains REVERT: A 63 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8380 (mt) REVERT: A 68 ASN cc_start: 0.8540 (m110) cc_final: 0.8153 (m-40) REVERT: A 121 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8124 (tp30) REVERT: A 243 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8479 (tt) REVERT: A 501 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7976 (t80) REVERT: A 566 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7408 (tt0) REVERT: B 173 ILE cc_start: 0.8558 (mm) cc_final: 0.7978 (mm) REVERT: B 183 ASN cc_start: 0.7018 (m-40) cc_final: 0.6112 (m110) REVERT: B 254 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8327 (t) REVERT: B 270 ASP cc_start: 0.7355 (t0) cc_final: 0.7013 (t0) REVERT: B 297 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.6920 (mt) REVERT: B 438 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6851 (mt-10) REVERT: B 480 HIS cc_start: 0.9200 (OUTLIER) cc_final: 0.8960 (p90) REVERT: B 501 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8306 (m-80) REVERT: B 515 ASP cc_start: 0.8251 (t0) cc_final: 0.7916 (m-30) REVERT: B 592 ASP cc_start: 0.8019 (p0) cc_final: 0.7723 (p0) outliers start: 48 outliers final: 35 residues processed: 156 average time/residue: 0.0933 time to fit residues: 21.6684 Evaluate side-chains 153 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 541 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 93 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 chunk 38 optimal weight: 0.0770 chunk 76 optimal weight: 0.9990 chunk 100 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.2538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 224 ASN B 304 GLN B 370 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.146981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.131274 restraints weight = 8789.514| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.38 r_work: 0.3271 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.003 0.029 9324 Z= 0.123 Angle : 0.535 6.352 12670 Z= 0.269 Chirality : 0.040 0.240 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.256 44.810 1262 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.01 % Allowed : 23.35 % Favored : 72.63 % 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: 0.86 (0.25), residues: 1176 helix: 1.26 (0.22), residues: 520 sheet: -2.74 (0.85), residues: 18 loop : 0.19 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.028 0.002 TYR B 341 PHE 0.010 0.001 PHE A 376 TRP 0.007 0.001 TRP B 331 HIS 0.004 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9322) covalent geometry : angle 0.53468 (12670) hydrogen bonds : bond 0.03718 ( 408) hydrogen bonds : angle 5.03690 ( 1200) Misc. bond : bond 0.00056 ( 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 161 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.395 Fit side-chains REVERT: A 68 ASN cc_start: 0.8469 (m110) cc_final: 0.8104 (m-40) REVERT: A 364 GLU cc_start: 0.7473 (tp30) cc_final: 0.6708 (tt0) REVERT: A 471 MET cc_start: 0.8021 (mtp) cc_final: 0.7558 (mtp) REVERT: A 501 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7891 (t80) REVERT: A 566 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: B 254 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8355 (t) REVERT: B 270 ASP cc_start: 0.7388 (t0) cc_final: 0.7017 (t0) REVERT: B 297 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.6804 (mt) REVERT: B 438 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6682 (mm-30) REVERT: B 480 HIS cc_start: 0.9166 (OUTLIER) cc_final: 0.8890 (p90) REVERT: B 501 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: B 515 ASP cc_start: 0.8214 (t0) cc_final: 0.7935 (m-30) REVERT: B 522 VAL cc_start: 0.8398 (m) cc_final: 0.8177 (m) REVERT: B 542 ASN cc_start: 0.8502 (m110) cc_final: 0.8184 (m-40) REVERT: B 592 ASP cc_start: 0.8034 (p0) cc_final: 0.7795 (p0) outliers start: 39 outliers final: 23 residues processed: 151 average time/residue: 0.0878 time to fit residues: 19.7904 Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 535 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 82 optimal weight: 0.0050 chunk 79 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 224 ASN B 370 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.144419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.128539 restraints weight = 8871.924| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.37 r_work: 0.3207 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9324 Z= 0.160 Angle : 0.554 6.710 12670 Z= 0.278 Chirality : 0.041 0.232 1404 Planarity : 0.005 0.058 1702 Dihedral : 4.277 45.428 1262 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.81 % Allowed : 23.56 % Favored : 72.63 % 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: 0.90 (0.25), residues: 1176 helix: 1.23 (0.22), residues: 512 sheet: -2.76 (0.83), residues: 18 loop : 0.31 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.031 0.003 TYR B 341 PHE 0.010 0.001 PHE B 501 TRP 0.008 0.001 TRP B 331 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9322) covalent geometry : angle 0.55372 (12670) hydrogen bonds : bond 0.03843 ( 408) hydrogen bonds : angle 5.07942 ( 1200) Misc. bond : bond 0.00039 ( 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 148 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 68 ASN cc_start: 0.8479 (m110) cc_final: 0.8178 (m-40) REVERT: A 137 GLU cc_start: 0.7838 (mp0) cc_final: 0.7389 (mp0) REVERT: A 471 MET cc_start: 0.8184 (mtp) cc_final: 0.7741 (mtp) REVERT: A 501 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7993 (t80) REVERT: A 566 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: B 254 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8377 (t) REVERT: B 270 ASP cc_start: 0.7472 (t0) cc_final: 0.7066 (t0) REVERT: B 297 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.6823 (mt) REVERT: B 438 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6717 (mm-30) REVERT: B 480 HIS cc_start: 0.9185 (OUTLIER) cc_final: 0.8943 (p90) REVERT: B 501 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: B 515 ASP cc_start: 0.8137 (t0) cc_final: 0.7813 (m-30) REVERT: B 592 ASP cc_start: 0.8043 (p0) cc_final: 0.7808 (p0) outliers start: 37 outliers final: 26 residues processed: 140 average time/residue: 0.0872 time to fit residues: 18.2789 Evaluate side-chains 138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 535 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 84 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN B 37 ASN B 68 ASN B 224 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.143245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.126963 restraints weight = 8884.084| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.40 r_work: 0.3192 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9324 Z= 0.166 Angle : 0.559 6.474 12670 Z= 0.282 Chirality : 0.041 0.222 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.308 45.826 1262 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.81 % Allowed : 23.66 % Favored : 72.53 % 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 (0.25), residues: 1176 helix: 1.20 (0.22), residues: 512 sheet: -2.83 (0.82), residues: 18 loop : 0.32 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.031 0.003 TYR B 341 PHE 0.011 0.001 PHE B 501 TRP 0.009 0.001 TRP B 331 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9322) covalent geometry : angle 0.55929 (12670) hydrogen bonds : bond 0.03877 ( 408) hydrogen bonds : angle 5.08316 ( 1200) Misc. bond : bond 0.00044 ( 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 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.348 Fit side-chains REVERT: A 68 ASN cc_start: 0.8521 (m110) cc_final: 0.8144 (m-40) REVERT: A 137 GLU cc_start: 0.7852 (mp0) cc_final: 0.7390 (mp0) REVERT: A 243 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 501 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7971 (t80) REVERT: A 566 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: B 137 GLU cc_start: 0.8050 (tt0) cc_final: 0.7809 (tt0) REVERT: B 254 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8361 (t) REVERT: B 270 ASP cc_start: 0.7498 (t0) cc_final: 0.7129 (t0) REVERT: B 297 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.6799 (mt) REVERT: B 438 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6744 (mm-30) REVERT: B 480 HIS cc_start: 0.9190 (OUTLIER) cc_final: 0.8943 (p90) REVERT: B 501 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: B 515 ASP cc_start: 0.8175 (t0) cc_final: 0.7833 (m-30) REVERT: B 592 ASP cc_start: 0.8033 (p0) cc_final: 0.7784 (p0) outliers start: 37 outliers final: 27 residues processed: 132 average time/residue: 0.0878 time to fit residues: 17.3551 Evaluate side-chains 137 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 501 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 88 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 68 ASN B 224 ASN ** B 370 GLN ** 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 = 0.3504 r_free = 0.3504 target = 0.141724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.126088 restraints weight = 8817.704| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.32 r_work: 0.3496 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9324 Z= 0.161 Angle : 0.556 6.425 12670 Z= 0.281 Chirality : 0.041 0.217 1404 Planarity : 0.005 0.058 1702 Dihedral : 4.326 46.179 1262 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.91 % Allowed : 23.66 % Favored : 72.43 % 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 (0.25), residues: 1176 helix: 1.19 (0.22), residues: 512 sheet: -2.97 (0.78), residues: 18 loop : 0.32 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.031 0.003 TYR B 341 PHE 0.011 0.001 PHE B 501 TRP 0.009 0.001 TRP B 331 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9322) covalent geometry : angle 0.55594 (12670) hydrogen bonds : bond 0.03870 ( 408) hydrogen bonds : angle 5.07565 ( 1200) Misc. bond : bond 0.00045 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.19 seconds wall clock time: 45 minutes 28.94 seconds (2728.94 seconds total)