Starting phenix.real_space_refine on Thu Mar 13 19:35:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjq_43291/03_2025/8vjq_43291.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjq_43291/03_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_43291/03_2025/8vjq_43291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjq_43291/03_2025/8vjq_43291.map" model { file = "/net/cci-nas-00/data/ceres_data/8vjq_43291/03_2025/8vjq_43291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjq_43291/03_2025/8vjq_43291.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 9.17, per 1000 atoms: 1.00 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: 3.06 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.00 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: 2.75 Time building geometry restraints manager: 3.14 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: 0.05 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: 8.390 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.290 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.560 ------------------------------------------------------------------------------- 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 : 0.010 0.361 9322 Z= 0.741 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (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 TRP 0.009 0.002 TRP B 110 HIS 0.021 0.002 HIS B 487 PHE 0.016 0.001 PHE A 376 TYR 0.048 0.003 TYR B 341 ARG 0.018 0.001 ARG A 397 *********************** 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 : 0.922 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: 0.2107 time to fit residues: 34.8262 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 : 1.037 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.139748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.125705 restraints weight = 8871.859| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.14 r_work: 0.3145 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9322 Z= 0.258 Angle : 0.571 6.545 12670 Z= 0.293 Chirality : 0.041 0.171 1404 Planarity : 0.006 0.068 1702 Dihedral : 4.396 41.185 1262 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.60 % Allowed : 21.50 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1176 helix: 0.95 (0.22), residues: 518 sheet: -1.87 (1.19), residues: 18 loop : -0.03 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 199 HIS 0.008 0.002 HIS A 487 PHE 0.014 0.001 PHE A 479 TYR 0.033 0.003 TYR A 341 ARG 0.008 0.001 ARG B 405 *********************** 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 166 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.973 Fit side-chains REVERT: A 243 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8470 (tt) REVERT: A 364 GLU cc_start: 0.7492 (tp30) cc_final: 0.6820 (tt0) REVERT: A 501 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7795 (t80) REVERT: B 173 ILE cc_start: 0.8432 (mm) cc_final: 0.7956 (mm) REVERT: B 183 ASN cc_start: 0.6918 (m-40) cc_final: 0.6486 (m110) REVERT: B 254 THR cc_start: 0.8663 (t) cc_final: 0.8434 (t) REVERT: B 438 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6845 (mt-10) REVERT: B 592 ASP cc_start: 0.8282 (p0) cc_final: 0.8019 (p0) outliers start: 35 outliers final: 18 residues processed: 155 average time/residue: 0.2173 time to fit residues: 47.5795 Evaluate side-chains 134 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 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 471 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 74 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 0.0370 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 224 ASN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.140292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.126315 restraints weight = 8985.090| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.15 r_work: 0.3195 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9322 Z= 0.228 Angle : 0.540 6.127 12670 Z= 0.274 Chirality : 0.040 0.173 1404 Planarity : 0.005 0.053 1702 Dihedral : 4.297 42.371 1262 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.91 % Allowed : 21.50 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1176 helix: 1.11 (0.22), residues: 520 sheet: -1.89 (1.09), residues: 18 loop : 0.09 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 199 HIS 0.007 0.002 HIS A 487 PHE 0.012 0.001 PHE A 479 TYR 0.030 0.003 TYR B 341 ARG 0.005 0.001 ARG B 320 *********************** 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 164 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 1.150 Fit side-chains REVERT: A 63 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8323 (mt) REVERT: A 243 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8460 (tt) REVERT: A 364 GLU cc_start: 0.7615 (tp30) cc_final: 0.6952 (tt0) REVERT: A 566 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: B 173 ILE cc_start: 0.8342 (mm) cc_final: 0.7852 (mm) REVERT: B 183 ASN cc_start: 0.6933 (m-40) cc_final: 0.6273 (m110) REVERT: B 254 THR cc_start: 0.8610 (t) cc_final: 0.8397 (t) REVERT: B 297 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.6960 (mt) REVERT: B 438 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6874 (mt-10) REVERT: B 592 ASP cc_start: 0.8270 (p0) cc_final: 0.8062 (p0) outliers start: 38 outliers final: 20 residues processed: 152 average time/residue: 0.2125 time to fit residues: 46.7784 Evaluate side-chains 136 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 259 THR 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 18 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 110 optimal weight: 0.0020 chunk 75 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 264 ASN B 127 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 = 0.3520 r_free = 0.3520 target = 0.143081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.127708 restraints weight = 8867.994| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.31 r_work: 0.3181 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9322 Z= 0.221 Angle : 0.533 6.128 12670 Z= 0.269 Chirality : 0.040 0.164 1404 Planarity : 0.005 0.054 1702 Dihedral : 4.243 43.156 1262 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.42 % Allowed : 21.50 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1176 helix: 1.18 (0.22), residues: 520 sheet: -2.34 (0.95), residues: 18 loop : 0.21 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 331 HIS 0.006 0.001 HIS A 487 PHE 0.010 0.001 PHE B 559 TYR 0.030 0.003 TYR B 341 ARG 0.004 0.000 ARG A 214 *********************** 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 167 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 1.084 Fit side-chains REVERT: A 243 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8485 (tt) REVERT: A 364 GLU cc_start: 0.7516 (tp30) cc_final: 0.6853 (tt0) REVERT: A 471 MET cc_start: 0.8107 (mtp) cc_final: 0.7596 (mtp) REVERT: A 501 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7886 (t80) REVERT: A 566 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: B 173 ILE cc_start: 0.8303 (mm) cc_final: 0.7789 (mm) REVERT: B 183 ASN cc_start: 0.6991 (m-40) cc_final: 0.6243 (m110) REVERT: B 254 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8314 (t) REVERT: B 297 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.6931 (mt) REVERT: B 438 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6868 (mt-10) REVERT: B 548 ASN cc_start: 0.8153 (m-40) cc_final: 0.7917 (m-40) REVERT: B 592 ASP cc_start: 0.8142 (p0) cc_final: 0.7895 (p0) outliers start: 43 outliers final: 26 residues processed: 155 average time/residue: 0.1895 time to fit residues: 42.9972 Evaluate side-chains 148 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 25 LEU 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 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 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 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 535 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 52 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 110 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 117 optimal weight: 0.1980 chunk 103 optimal weight: 0.6980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 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 = 0.3574 r_free = 0.3574 target = 0.147151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.131433 restraints weight = 8900.991| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.38 r_work: 0.3242 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9322 Z= 0.190 Angle : 0.519 5.982 12670 Z= 0.263 Chirality : 0.039 0.141 1404 Planarity : 0.004 0.054 1702 Dihedral : 4.206 43.841 1262 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.32 % Allowed : 21.71 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1176 helix: 1.28 (0.22), residues: 520 sheet: -2.59 (0.89), residues: 18 loop : 0.25 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 PHE 0.010 0.001 PHE A 376 TYR 0.029 0.002 TYR B 341 ARG 0.005 0.000 ARG A 214 *********************** 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 165 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.963 Fit side-chains REVERT: A 243 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8455 (tt) REVERT: A 364 GLU cc_start: 0.7526 (tp30) cc_final: 0.6807 (tt0) REVERT: A 501 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7834 (t80) REVERT: A 566 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: B 13 LYS cc_start: 0.7950 (tptp) cc_final: 0.7426 (tptt) REVERT: B 254 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8323 (t) REVERT: B 297 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.6860 (mt) REVERT: B 438 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6795 (mm-30) REVERT: B 501 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: B 510 GLN cc_start: 0.7919 (mm110) cc_final: 0.7701 (mm110) REVERT: B 542 ASN cc_start: 0.8486 (m110) cc_final: 0.8176 (m-40) REVERT: B 592 ASP cc_start: 0.8113 (p0) cc_final: 0.7848 (p0) outliers start: 42 outliers final: 26 residues processed: 155 average time/residue: 0.1955 time to fit residues: 43.9786 Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU 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 541 ASP 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 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 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 471 MET 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 15 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 chunk 70 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 B 68 ASN B 127 ASN B 224 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 = 0.3564 r_free = 0.3564 target = 0.145934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.129995 restraints weight = 8760.824| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.38 r_work: 0.3209 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9322 Z= 0.230 Angle : 0.533 6.165 12670 Z= 0.270 Chirality : 0.040 0.168 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.228 44.150 1262 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.14 % Allowed : 21.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1176 helix: 1.29 (0.23), residues: 512 sheet: -2.75 (0.83), residues: 18 loop : 0.31 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 PHE 0.014 0.001 PHE B 376 TYR 0.030 0.003 TYR B 341 ARG 0.005 0.000 ARG A 214 *********************** 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 170 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 120 time to evaluate : 0.956 Fit side-chains REVERT: A 68 ASN cc_start: 0.8475 (m110) cc_final: 0.8100 (m-40) REVERT: A 243 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 364 GLU cc_start: 0.7500 (tp30) cc_final: 0.6790 (tt0) REVERT: A 501 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7945 (t80) REVERT: A 566 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: B 13 LYS cc_start: 0.7912 (tptp) cc_final: 0.7346 (tptt) REVERT: B 254 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8314 (t) REVERT: B 297 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.6870 (mt) REVERT: B 370 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8716 (tp40) REVERT: B 438 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6780 (mm-30) REVERT: B 480 HIS cc_start: 0.9218 (OUTLIER) cc_final: 0.8946 (p90) REVERT: B 501 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: B 510 GLN cc_start: 0.8043 (mm110) cc_final: 0.7804 (mm110) REVERT: B 542 ASN cc_start: 0.8513 (m110) cc_final: 0.8201 (m-40) REVERT: B 592 ASP cc_start: 0.8078 (p0) cc_final: 0.7814 (p0) outliers start: 50 outliers final: 32 residues processed: 160 average time/residue: 0.1808 time to fit residues: 42.6766 Evaluate side-chains 151 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 143 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 68 ASN B 224 ASN B 304 GLN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3554 r_free = 0.3554 target = 0.144997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.128999 restraints weight = 8910.889| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.38 r_work: 0.3197 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9322 Z= 0.243 Angle : 0.546 8.265 12670 Z= 0.275 Chirality : 0.041 0.223 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.253 44.616 1262 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.73 % Allowed : 21.60 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1176 helix: 1.27 (0.22), residues: 512 sheet: -2.84 (0.79), residues: 18 loop : 0.30 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 PHE 0.012 0.001 PHE B 376 TYR 0.030 0.003 TYR B 341 ARG 0.005 0.000 ARG A 214 *********************** 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 161 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 0.993 Fit side-chains REVERT: A 68 ASN cc_start: 0.8525 (m110) cc_final: 0.8128 (m-40) REVERT: A 102 ASP cc_start: 0.7506 (t0) cc_final: 0.7058 (t0) REVERT: A 243 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8464 (tt) REVERT: A 480 HIS cc_start: 0.9261 (OUTLIER) cc_final: 0.8919 (p90) REVERT: A 501 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7954 (t80) REVERT: A 566 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: B 13 LYS cc_start: 0.7789 (tptp) cc_final: 0.7181 (tptt) REVERT: B 254 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8349 (t) REVERT: B 297 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.6846 (mt) REVERT: B 438 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6786 (mm-30) REVERT: B 480 HIS cc_start: 0.9220 (OUTLIER) cc_final: 0.8983 (p90) REVERT: B 501 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: B 592 ASP cc_start: 0.8077 (p0) cc_final: 0.7835 (p0) outliers start: 46 outliers final: 32 residues processed: 152 average time/residue: 0.1785 time to fit residues: 40.4840 Evaluate side-chains 150 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 480 HIS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 12 optimal weight: 0.0570 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 68 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.145549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129641 restraints weight = 9037.822| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.37 r_work: 0.3208 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9322 Z= 0.229 Angle : 0.544 7.798 12670 Z= 0.274 Chirality : 0.040 0.213 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.246 45.201 1262 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.25 % Allowed : 21.60 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1176 helix: 1.29 (0.23), residues: 512 sheet: -2.96 (0.76), residues: 18 loop : 0.30 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 331 HIS 0.004 0.001 HIS A 487 PHE 0.011 0.001 PHE B 376 TYR 0.030 0.003 TYR B 341 ARG 0.005 0.000 ARG A 214 *********************** 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 178 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 1.055 Fit side-chains REVERT: A 68 ASN cc_start: 0.8505 (m110) cc_final: 0.8122 (m-40) REVERT: A 102 ASP cc_start: 0.7501 (t0) cc_final: 0.7071 (t0) REVERT: A 137 GLU cc_start: 0.7846 (mp0) cc_final: 0.7359 (mp0) REVERT: A 243 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 480 HIS cc_start: 0.9239 (OUTLIER) cc_final: 0.8848 (p90) REVERT: A 501 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7972 (t80) REVERT: A 566 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: B 13 LYS cc_start: 0.7813 (tptp) cc_final: 0.7212 (tptt) REVERT: B 254 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8384 (t) REVERT: B 370 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8757 (tp40) REVERT: B 438 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6746 (mm-30) REVERT: B 480 HIS cc_start: 0.9209 (OUTLIER) cc_final: 0.8942 (p90) REVERT: B 501 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: B 542 ASN cc_start: 0.8521 (m110) cc_final: 0.8240 (m-40) REVERT: B 592 ASP cc_start: 0.8075 (p0) cc_final: 0.7806 (p0) outliers start: 51 outliers final: 32 residues processed: 167 average time/residue: 0.1709 time to fit residues: 42.6884 Evaluate side-chains 158 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 356 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 480 HIS 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 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 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 254 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 0.0030 chunk 88 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.145048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.129086 restraints weight = 8873.839| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.38 r_work: 0.3203 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 0.035 9322 Z= 0.245 Angle : 0.560 7.648 12670 Z= 0.281 Chirality : 0.041 0.197 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.281 45.478 1262 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.32 % Allowed : 22.63 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1176 helix: 1.21 (0.23), residues: 514 sheet: -2.97 (0.76), residues: 18 loop : 0.31 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 331 HIS 0.004 0.001 HIS A 487 PHE 0.011 0.001 PHE B 501 TYR 0.030 0.003 TYR B 341 ARG 0.006 0.000 ARG A 214 *********************** 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 154 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 1.091 Fit side-chains REVERT: A 68 ASN cc_start: 0.8510 (m110) cc_final: 0.8128 (m-40) REVERT: A 102 ASP cc_start: 0.7509 (t0) cc_final: 0.7084 (t0) REVERT: A 137 GLU cc_start: 0.7848 (mp0) cc_final: 0.7377 (mp0) REVERT: A 243 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 480 HIS cc_start: 0.9254 (OUTLIER) cc_final: 0.8864 (p90) REVERT: A 501 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7989 (t80) REVERT: A 566 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: B 137 GLU cc_start: 0.8069 (tt0) cc_final: 0.7829 (tt0) REVERT: B 254 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8364 (t) REVERT: B 438 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6734 (mm-30) REVERT: B 480 HIS cc_start: 0.9214 (OUTLIER) cc_final: 0.8981 (p90) REVERT: B 501 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: B 515 ASP cc_start: 0.8260 (t0) cc_final: 0.7896 (m-30) REVERT: B 592 ASP cc_start: 0.8057 (p0) cc_final: 0.7807 (p0) outliers start: 42 outliers final: 34 residues processed: 146 average time/residue: 0.1824 time to fit residues: 39.7845 Evaluate side-chains 151 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 173 ILE 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 480 HIS 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 254 THR 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 74 optimal weight: 0.5980 chunk 113 optimal weight: 0.0770 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 104 optimal weight: 0.0770 chunk 116 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 38 optimal weight: 0.0570 chunk 7 optimal weight: 0.7980 overall best weight: 0.3014 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.148543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.132819 restraints weight = 8932.841| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.38 r_work: 0.3259 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9322 Z= 0.183 Angle : 0.536 7.215 12670 Z= 0.268 Chirality : 0.040 0.200 1404 Planarity : 0.004 0.055 1702 Dihedral : 4.208 46.507 1262 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.32 % Allowed : 22.74 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1176 helix: 1.38 (0.23), residues: 514 sheet: -3.03 (0.77), residues: 18 loop : 0.36 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 331 HIS 0.004 0.001 HIS A 487 PHE 0.010 0.001 PHE B 376 TYR 0.029 0.002 TYR B 341 ARG 0.006 0.000 ARG A 214 ********************** 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 153 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 1.079 Fit side-chains REVERT: A 243 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8385 (tt) REVERT: A 480 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8774 (p90) REVERT: A 501 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7897 (t80) REVERT: A 518 GLU cc_start: 0.7690 (tt0) cc_final: 0.7386 (tp30) REVERT: A 566 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: B 254 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8392 (t) REVERT: B 438 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6720 (mm-30) REVERT: B 480 HIS cc_start: 0.9169 (OUTLIER) cc_final: 0.8911 (p90) REVERT: B 501 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8221 (m-80) REVERT: B 515 ASP cc_start: 0.8180 (t0) cc_final: 0.7878 (m-30) REVERT: B 542 ASN cc_start: 0.8504 (m110) cc_final: 0.8181 (m-40) REVERT: B 592 ASP cc_start: 0.8018 (p0) cc_final: 0.7806 (p0) outliers start: 42 outliers final: 31 residues processed: 143 average time/residue: 0.1855 time to fit residues: 39.1442 Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 173 ILE 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 390 THR Chi-restraints excluded: chain A residue 480 HIS 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 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 63 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 75 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.147117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131297 restraints weight = 8885.414| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.38 r_work: 0.3231 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9322 Z= 0.215 Angle : 0.543 7.258 12670 Z= 0.273 Chirality : 0.040 0.189 1404 Planarity : 0.005 0.058 1702 Dihedral : 4.231 46.774 1262 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.42 % Allowed : 22.22 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1176 helix: 1.32 (0.23), residues: 514 sheet: -3.08 (0.76), residues: 18 loop : 0.35 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 331 HIS 0.004 0.001 HIS A 487 PHE 0.010 0.001 PHE B 376 TYR 0.030 0.002 TYR B 341 ARG 0.006 0.000 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5110.03 seconds wall clock time: 90 minutes 26.10 seconds (5426.10 seconds total)