Starting phenix.real_space_refine on Fri Aug 22 19:29:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wns_37671/08_2025/8wns_37671.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wns_37671/08_2025/8wns_37671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wns_37671/08_2025/8wns_37671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wns_37671/08_2025/8wns_37671.map" model { file = "/net/cci-nas-00/data/ceres_data/8wns_37671/08_2025/8wns_37671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wns_37671/08_2025/8wns_37671.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.079 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4710 2.51 5 N 1189 2.21 5 O 1295 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7226 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3645 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Chain: "B" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3525 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 23, 'TRANS': 432} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.97, per 1000 atoms: 0.27 Number of scatterers: 7226 At special positions: 0 Unit cell: (103.265, 79.351, 120.657, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1295 8.00 N 1189 7.00 C 4710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 154 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 366 " " NAG A 702 " - " ASN A 382 " " NAG A 703 " - " ASN A 425 " " NAG A 704 " - " ASN A 507 " Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 426.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 63.5% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 178 through 207 removed outlier: 3.713A pdb=" N THR A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.823A pdb=" N HIS A 221 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.623A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 324 through 342 Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.922A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 394 removed outlier: 3.848A pdb=" N ILE A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.568A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 461 removed outlier: 4.087A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 534 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.837A pdb=" N SER A 589 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 54 Processing helix chain 'B' and resid 60 through 70 removed outlier: 4.209A pdb=" N GLY B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 100 removed outlier: 3.526A pdb=" N ALA B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 115 through 129 Processing helix chain 'B' and resid 129 through 148 Processing helix chain 'B' and resid 157 through 179 removed outlier: 3.683A pdb=" N SER B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 212 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 247 through 255 removed outlier: 4.036A pdb=" N LEU B 251 " --> pdb=" O TRP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 291 removed outlier: 3.568A pdb=" N ASN B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Proline residue: B 266 - end of helix Proline residue: B 274 - end of helix Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 301 through 311 removed outlier: 3.596A pdb=" N THR B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 315 Processing helix chain 'B' and resid 316 through 348 removed outlier: 4.244A pdb=" N VAL B 320 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 364 through 380 removed outlier: 3.560A pdb=" N LEU B 368 " --> pdb=" O PRO B 364 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 413 Processing helix chain 'B' and resid 424 through 445 Processing helix chain 'B' and resid 445 through 458 removed outlier: 4.450A pdb=" N CYS B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 removed outlier: 4.029A pdb=" N ILE B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.456A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY A 345 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 307 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU A 260 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP A 308 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 262 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 261 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU A 225 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 removed outlier: 7.024A pdb=" N GLN A 280 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 543 removed outlier: 3.506A pdb=" N LEU A 598 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA6, first strand: chain 'B' and resid 357 through 358 430 hydrogen bonds defined for protein. 1242 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: 1.30 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2251 1.34 - 1.46: 1758 1.46 - 1.58: 3354 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 7413 Sorted by residual: bond pdb=" N GLU A 472 " pdb=" CA GLU A 472 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.16e+00 bond pdb=" N THR A 276 " pdb=" CA THR A 276 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.53e+00 bond pdb=" N SER B 315 " pdb=" CA SER B 315 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.40e+00 bond pdb=" N SER A 536 " pdb=" CA SER A 536 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.23e+00 bond pdb=" CA SER B 315 " pdb=" CB SER B 315 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.64e-02 3.72e+03 4.59e+00 ... (remaining 7408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 9881 1.88 - 3.76: 160 3.76 - 5.64: 34 5.64 - 7.51: 13 7.51 - 9.39: 4 Bond angle restraints: 10092 Sorted by residual: angle pdb=" N MET B 291 " pdb=" CA MET B 291 " pdb=" C MET B 291 " ideal model delta sigma weight residual 108.34 113.18 -4.84 1.31e+00 5.83e-01 1.36e+01 angle pdb=" N GLY B 382 " pdb=" CA GLY B 382 " pdb=" C GLY B 382 " ideal model delta sigma weight residual 111.20 115.64 -4.44 1.39e+00 5.18e-01 1.02e+01 angle pdb=" CB MET B 227 " pdb=" CG MET B 227 " pdb=" SD MET B 227 " ideal model delta sigma weight residual 112.70 121.66 -8.96 3.00e+00 1.11e-01 8.92e+00 angle pdb=" CA LEU A 307 " pdb=" CB LEU A 307 " pdb=" CG LEU A 307 " ideal model delta sigma weight residual 116.30 125.69 -9.39 3.50e+00 8.16e-02 7.20e+00 angle pdb=" CA LEU B 117 " pdb=" CB LEU B 117 " pdb=" CG LEU B 117 " ideal model delta sigma weight residual 116.30 125.30 -9.00 3.50e+00 8.16e-02 6.61e+00 ... (remaining 10087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3720 17.53 - 35.06: 493 35.06 - 52.59: 126 52.59 - 70.12: 26 70.12 - 87.66: 5 Dihedral angle restraints: 4370 sinusoidal: 1734 harmonic: 2636 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 154 " pdb=" CB CYS B 154 " ideal model delta sinusoidal sigma weight residual -86.00 -145.51 59.51 1 1.00e+01 1.00e-02 4.73e+01 dihedral pdb=" CA GLU B 257 " pdb=" C GLU B 257 " pdb=" N MET B 258 " pdb=" CA MET B 258 " ideal model delta harmonic sigma weight residual 180.00 161.01 18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CG ARG B 360 " pdb=" CD ARG B 360 " pdb=" NE ARG B 360 " pdb=" CZ ARG B 360 " ideal model delta sinusoidal sigma weight residual 90.00 134.29 -44.29 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 4367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 865 0.040 - 0.081: 227 0.081 - 0.121: 65 0.121 - 0.162: 5 0.162 - 0.202: 3 Chirality restraints: 1165 Sorted by residual: chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 382 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CG LEU A 339 " pdb=" CB LEU A 339 " pdb=" CD1 LEU A 339 " pdb=" CD2 LEU A 339 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.56e-01 ... (remaining 1162 not shown) Planarity restraints: 1261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 469 " -0.017 2.00e-02 2.50e+03 1.39e-02 4.85e+00 pdb=" CG TRP B 469 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 469 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 469 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 469 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 469 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 469 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 469 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 469 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 469 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 337 " 0.013 2.00e-02 2.50e+03 1.43e-02 4.11e+00 pdb=" CG TYR B 337 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 337 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 337 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 337 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 337 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 337 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 337 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 350 " 0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO B 351 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 351 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 351 " 0.024 5.00e-02 4.00e+02 ... (remaining 1258 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 814 2.75 - 3.28: 7218 3.28 - 3.82: 12320 3.82 - 4.36: 13302 4.36 - 4.90: 23556 Nonbonded interactions: 57210 Sorted by model distance: nonbonded pdb=" O GLY A 463 " pdb=" NH2 ARG A 531 " model vdw 2.207 3.120 nonbonded pdb=" O LYS A 417 " pdb=" OG1 THR A 421 " model vdw 2.215 3.040 nonbonded pdb=" O HIS A 266 " pdb=" OH TYR A 313 " model vdw 2.226 3.040 nonbonded pdb=" O SER A 582 " pdb=" OG SER A 582 " model vdw 2.255 3.040 nonbonded pdb=" NH1 ARG A 535 " pdb=" OD1 ASN B 153 " model vdw 2.259 3.120 ... (remaining 57205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.460 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.070 Find NCS groups from input model: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 0.003 0.037 7418 Z= 0.156 Angle : 0.648 9.392 10106 Z= 0.311 Chirality : 0.040 0.202 1165 Planarity : 0.004 0.043 1257 Dihedral : 16.657 87.656 2679 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.39 % Allowed : 30.06 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 1.29 (0.28), residues: 920 helix: 1.76 (0.22), residues: 547 sheet: 0.80 (0.78), residues: 57 loop : -0.75 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.033 0.001 TYR B 337 PHE 0.015 0.001 PHE A 542 TRP 0.037 0.001 TRP B 469 HIS 0.004 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7413) covalent geometry : angle 0.64647 (10092) SS BOND : bond 0.00099 ( 1) SS BOND : angle 1.19469 ( 2) hydrogen bonds : bond 0.16297 ( 430) hydrogen bonds : angle 5.83908 ( 1242) link_NAG-ASN : bond 0.00301 ( 4) link_NAG-ASN : angle 1.18693 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.317 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 106 average time/residue: 0.0672 time to fit residues: 10.6987 Evaluate side-chains 104 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain B residue 81 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0020 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** B 358 HIS ** 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 = 0.4382 r_free = 0.4382 target = 0.188451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.123084 restraints weight = 10455.457| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 4.16 r_work: 0.3388 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7418 Z= 0.135 Angle : 0.621 12.655 10106 Z= 0.294 Chirality : 0.040 0.215 1165 Planarity : 0.004 0.043 1257 Dihedral : 4.395 57.623 1073 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.48 % Allowed : 26.32 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 1.55 (0.28), residues: 920 helix: 2.06 (0.22), residues: 544 sheet: 0.48 (0.73), residues: 62 loop : -0.71 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.019 0.001 TYR B 337 PHE 0.020 0.001 PHE B 442 TRP 0.016 0.001 TRP B 469 HIS 0.002 0.000 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7413) covalent geometry : angle 0.61890 (10092) SS BOND : bond 0.00415 ( 1) SS BOND : angle 1.99050 ( 2) hydrogen bonds : bond 0.04431 ( 430) hydrogen bonds : angle 4.30440 ( 1242) link_NAG-ASN : bond 0.00332 ( 4) link_NAG-ASN : angle 1.38215 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8327 (t0) cc_final: 0.7777 (t0) REVERT: A 339 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6492 (mm) REVERT: A 360 PHE cc_start: 0.7862 (m-80) cc_final: 0.7542 (m-80) REVERT: B 145 TYR cc_start: 0.8541 (m-80) cc_final: 0.7936 (m-80) REVERT: B 304 VAL cc_start: 0.8154 (m) cc_final: 0.7910 (m) outliers start: 27 outliers final: 14 residues processed: 128 average time/residue: 0.0675 time to fit residues: 12.6908 Evaluate side-chains 117 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 407 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.0470 chunk 4 optimal weight: 0.0170 chunk 41 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 0.0870 chunk 77 optimal weight: 7.9990 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS B 294 GLN ** B 358 HIS ** 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 = 0.4401 r_free = 0.4401 target = 0.190104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.126122 restraints weight = 10399.585| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 4.03 r_work: 0.3421 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7418 Z= 0.113 Angle : 0.567 10.847 10106 Z= 0.272 Chirality : 0.038 0.169 1165 Planarity : 0.004 0.044 1257 Dihedral : 3.791 16.348 1070 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.48 % Allowed : 25.42 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 1.66 (0.29), residues: 920 helix: 2.17 (0.23), residues: 540 sheet: 0.49 (0.73), residues: 62 loop : -0.66 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 207 TYR 0.016 0.001 TYR B 337 PHE 0.015 0.001 PHE B 327 TRP 0.019 0.001 TRP B 469 HIS 0.004 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7413) covalent geometry : angle 0.56505 (10092) SS BOND : bond 0.00236 ( 1) SS BOND : angle 1.55594 ( 2) hydrogen bonds : bond 0.03647 ( 430) hydrogen bonds : angle 3.98213 ( 1242) link_NAG-ASN : bond 0.00268 ( 4) link_NAG-ASN : angle 1.27723 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8299 (t0) cc_final: 0.7606 (t0) REVERT: A 339 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6364 (mm) REVERT: A 360 PHE cc_start: 0.7828 (m-80) cc_final: 0.7487 (m-80) REVERT: A 610 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7470 (tp) REVERT: B 92 CYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8200 (t) REVERT: B 145 TYR cc_start: 0.8558 (m-80) cc_final: 0.7935 (m-80) REVERT: B 281 THR cc_start: 0.8514 (m) cc_final: 0.8143 (p) outliers start: 27 outliers final: 10 residues processed: 143 average time/residue: 0.0604 time to fit residues: 13.1497 Evaluate side-chains 119 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 394 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 54 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 chunk 12 optimal weight: 0.0020 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.0010 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 HIS ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.196621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135314 restraints weight = 10410.957| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.67 r_work: 0.3528 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7418 Z= 0.111 Angle : 0.577 9.787 10106 Z= 0.275 Chirality : 0.039 0.192 1165 Planarity : 0.004 0.045 1257 Dihedral : 3.730 16.743 1070 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.10 % Allowed : 26.58 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 1.66 (0.28), residues: 920 helix: 2.16 (0.23), residues: 539 sheet: 0.52 (0.73), residues: 62 loop : -0.65 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 207 TYR 0.031 0.001 TYR B 337 PHE 0.014 0.001 PHE B 327 TRP 0.020 0.001 TRP B 469 HIS 0.010 0.001 HIS B 485 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7413) covalent geometry : angle 0.57561 (10092) SS BOND : bond 0.00169 ( 1) SS BOND : angle 1.43185 ( 2) hydrogen bonds : bond 0.03467 ( 430) hydrogen bonds : angle 3.90369 ( 1242) link_NAG-ASN : bond 0.00243 ( 4) link_NAG-ASN : angle 1.18324 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 GLU cc_start: 0.8575 (pm20) cc_final: 0.8352 (tm-30) REVERT: A 339 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6312 (mm) REVERT: A 360 PHE cc_start: 0.7848 (m-80) cc_final: 0.7509 (m-80) REVERT: A 610 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7528 (tp) REVERT: B 92 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8204 (t) REVERT: B 145 TYR cc_start: 0.8612 (m-80) cc_final: 0.7898 (m-80) REVERT: B 434 TRP cc_start: 0.8047 (t60) cc_final: 0.7801 (t60) REVERT: B 442 PHE cc_start: 0.7806 (m-80) cc_final: 0.7512 (m-80) outliers start: 24 outliers final: 16 residues processed: 134 average time/residue: 0.0657 time to fit residues: 13.1406 Evaluate side-chains 122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 34 optimal weight: 0.0010 chunk 35 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 overall best weight: 0.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 HIS ** B 358 HIS ** 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 = 0.4414 r_free = 0.4414 target = 0.191059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.130904 restraints weight = 10312.917| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.82 r_work: 0.3456 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7418 Z= 0.109 Angle : 0.565 9.437 10106 Z= 0.270 Chirality : 0.039 0.155 1165 Planarity : 0.004 0.045 1257 Dihedral : 3.764 19.809 1070 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.00 % Allowed : 25.29 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 1.72 (0.29), residues: 920 helix: 2.20 (0.23), residues: 539 sheet: 0.58 (0.71), residues: 62 loop : -0.61 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 210 TYR 0.022 0.001 TYR B 337 PHE 0.018 0.001 PHE A 337 TRP 0.022 0.001 TRP B 469 HIS 0.005 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7413) covalent geometry : angle 0.56341 (10092) SS BOND : bond 0.00307 ( 1) SS BOND : angle 1.83414 ( 2) hydrogen bonds : bond 0.03321 ( 430) hydrogen bonds : angle 3.82563 ( 1242) link_NAG-ASN : bond 0.00232 ( 4) link_NAG-ASN : angle 1.15608 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 GLU cc_start: 0.8577 (pm20) cc_final: 0.8354 (tm-30) REVERT: A 339 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6281 (mm) REVERT: A 360 PHE cc_start: 0.7871 (m-80) cc_final: 0.7587 (m-80) REVERT: A 610 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7504 (tp) REVERT: B 92 CYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8387 (t) REVERT: B 128 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8759 (mm) REVERT: B 145 TYR cc_start: 0.8552 (m-80) cc_final: 0.7807 (m-80) REVERT: B 442 PHE cc_start: 0.7930 (m-80) cc_final: 0.7641 (m-80) outliers start: 31 outliers final: 19 residues processed: 138 average time/residue: 0.0619 time to fit residues: 12.8689 Evaluate side-chains 127 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 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 = 0.4435 r_free = 0.4435 target = 0.191977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.130997 restraints weight = 10438.772| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.86 r_work: 0.3457 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7418 Z= 0.141 Angle : 0.606 9.077 10106 Z= 0.290 Chirality : 0.040 0.157 1165 Planarity : 0.004 0.044 1257 Dihedral : 4.020 40.626 1070 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.77 % Allowed : 25.94 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.66 (0.28), residues: 920 helix: 2.18 (0.23), residues: 540 sheet: 0.45 (0.71), residues: 62 loop : -0.68 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 207 TYR 0.036 0.002 TYR B 337 PHE 0.016 0.001 PHE B 327 TRP 0.023 0.001 TRP B 469 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7413) covalent geometry : angle 0.60259 (10092) SS BOND : bond 0.01016 ( 1) SS BOND : angle 3.97646 ( 2) hydrogen bonds : bond 0.03536 ( 430) hydrogen bonds : angle 3.87837 ( 1242) link_NAG-ASN : bond 0.00235 ( 4) link_NAG-ASN : angle 1.20447 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8269 (t0) cc_final: 0.7826 (t0) REVERT: A 339 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6332 (mm) REVERT: A 360 PHE cc_start: 0.7818 (m-80) cc_final: 0.7524 (m-80) REVERT: A 610 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7534 (tp) REVERT: B 92 CYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8420 (t) REVERT: B 128 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8797 (mm) REVERT: B 145 TYR cc_start: 0.8677 (m-80) cc_final: 0.7963 (m-80) REVERT: B 442 PHE cc_start: 0.7952 (m-80) cc_final: 0.7654 (m-80) outliers start: 37 outliers final: 23 residues processed: 134 average time/residue: 0.0639 time to fit residues: 12.8962 Evaluate side-chains 128 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 407 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 42 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.191673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.130861 restraints weight = 10472.617| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 4.07 r_work: 0.3409 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7418 Z= 0.143 Angle : 0.621 9.187 10106 Z= 0.294 Chirality : 0.040 0.162 1165 Planarity : 0.004 0.043 1257 Dihedral : 3.970 34.224 1070 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.39 % Allowed : 25.81 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.64 (0.28), residues: 920 helix: 2.20 (0.23), residues: 539 sheet: 0.30 (0.72), residues: 62 loop : -0.70 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 207 TYR 0.030 0.002 TYR B 337 PHE 0.025 0.001 PHE B 433 TRP 0.019 0.001 TRP B 469 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7413) covalent geometry : angle 0.61848 (10092) SS BOND : bond 0.00755 ( 1) SS BOND : angle 2.72296 ( 2) hydrogen bonds : bond 0.03575 ( 430) hydrogen bonds : angle 3.85168 ( 1242) link_NAG-ASN : bond 0.00243 ( 4) link_NAG-ASN : angle 1.20753 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8354 (t0) cc_final: 0.7842 (t0) REVERT: A 339 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6391 (mm) REVERT: A 360 PHE cc_start: 0.7819 (m-80) cc_final: 0.7533 (m-80) REVERT: B 92 CYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8533 (t) REVERT: B 145 TYR cc_start: 0.8719 (m-80) cc_final: 0.8016 (m-80) REVERT: B 258 MET cc_start: 0.5865 (pmm) cc_final: 0.5407 (pmm) REVERT: B 447 MET cc_start: 0.6347 (tpp) cc_final: 0.5772 (tpp) outliers start: 34 outliers final: 21 residues processed: 133 average time/residue: 0.0619 time to fit residues: 12.6760 Evaluate side-chains 125 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 0.0170 chunk 36 optimal weight: 0.5980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.197010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.134127 restraints weight = 10426.252| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.91 r_work: 0.3491 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7418 Z= 0.131 Angle : 0.633 9.662 10106 Z= 0.296 Chirality : 0.041 0.231 1165 Planarity : 0.004 0.043 1257 Dihedral : 3.911 29.798 1070 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.39 % Allowed : 26.45 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 1.65 (0.28), residues: 920 helix: 2.22 (0.23), residues: 538 sheet: 0.29 (0.71), residues: 62 loop : -0.71 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 207 TYR 0.029 0.002 TYR B 337 PHE 0.015 0.001 PHE B 327 TRP 0.028 0.001 TRP B 469 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7413) covalent geometry : angle 0.63182 (10092) SS BOND : bond 0.00423 ( 1) SS BOND : angle 1.70537 ( 2) hydrogen bonds : bond 0.03508 ( 430) hydrogen bonds : angle 3.83753 ( 1242) link_NAG-ASN : bond 0.00246 ( 4) link_NAG-ASN : angle 1.19958 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8309 (t0) cc_final: 0.7810 (t0) REVERT: A 339 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6425 (mm) REVERT: A 360 PHE cc_start: 0.7868 (m-80) cc_final: 0.7572 (m-80) REVERT: B 92 CYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8557 (t) REVERT: B 145 TYR cc_start: 0.8769 (m-80) cc_final: 0.8103 (m-80) REVERT: B 189 MET cc_start: 0.8819 (tmm) cc_final: 0.8590 (tmm) REVERT: B 258 MET cc_start: 0.5811 (pmm) cc_final: 0.5372 (pmm) REVERT: B 431 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8516 (pp) outliers start: 34 outliers final: 21 residues processed: 133 average time/residue: 0.0603 time to fit residues: 12.2942 Evaluate side-chains 129 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 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 = 0.4499 r_free = 0.4499 target = 0.199854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133050 restraints weight = 10457.809| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.71 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7418 Z= 0.141 Angle : 0.643 9.958 10106 Z= 0.300 Chirality : 0.041 0.187 1165 Planarity : 0.004 0.046 1257 Dihedral : 3.907 26.191 1070 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.61 % Allowed : 27.10 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 1.62 (0.29), residues: 920 helix: 2.23 (0.23), residues: 538 sheet: 0.19 (0.72), residues: 62 loop : -0.78 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 207 TYR 0.026 0.002 TYR B 337 PHE 0.015 0.001 PHE B 327 TRP 0.025 0.001 TRP B 469 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7413) covalent geometry : angle 0.64181 (10092) SS BOND : bond 0.00434 ( 1) SS BOND : angle 1.64854 ( 2) hydrogen bonds : bond 0.03590 ( 430) hydrogen bonds : angle 3.83035 ( 1242) link_NAG-ASN : bond 0.00244 ( 4) link_NAG-ASN : angle 1.18594 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8327 (t0) cc_final: 0.7909 (t0) REVERT: A 339 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6574 (mm) REVERT: A 360 PHE cc_start: 0.7853 (m-80) cc_final: 0.7543 (m-80) REVERT: B 92 CYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8616 (t) REVERT: B 145 TYR cc_start: 0.8528 (m-80) cc_final: 0.7770 (m-80) REVERT: B 154 CYS cc_start: 0.5719 (OUTLIER) cc_final: 0.5057 (m) REVERT: B 189 MET cc_start: 0.8876 (tmm) cc_final: 0.8674 (tmm) REVERT: B 258 MET cc_start: 0.5848 (pmm) cc_final: 0.5508 (pmm) outliers start: 28 outliers final: 20 residues processed: 127 average time/residue: 0.0602 time to fit residues: 11.8420 Evaluate side-chains 124 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain B residue 394 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.0770 chunk 74 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 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 = 0.4461 r_free = 0.4461 target = 0.193704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134835 restraints weight = 10343.290| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.44 r_work: 0.3481 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7418 Z= 0.116 Angle : 0.640 10.242 10106 Z= 0.295 Chirality : 0.040 0.164 1165 Planarity : 0.004 0.044 1257 Dihedral : 3.838 24.146 1070 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.35 % Allowed : 27.61 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 1.60 (0.28), residues: 920 helix: 2.21 (0.23), residues: 538 sheet: 0.19 (0.71), residues: 62 loop : -0.78 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 207 TYR 0.028 0.001 TYR B 337 PHE 0.014 0.001 PHE A 542 TRP 0.031 0.001 TRP B 469 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7413) covalent geometry : angle 0.63921 (10092) SS BOND : bond 0.00476 ( 1) SS BOND : angle 1.39513 ( 2) hydrogen bonds : bond 0.03410 ( 430) hydrogen bonds : angle 3.76063 ( 1242) link_NAG-ASN : bond 0.00244 ( 4) link_NAG-ASN : angle 1.15209 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8332 (t0) cc_final: 0.7868 (t0) REVERT: A 339 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6363 (mm) REVERT: B 92 CYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8541 (t) REVERT: B 145 TYR cc_start: 0.8746 (m-80) cc_final: 0.8088 (m-80) REVERT: B 154 CYS cc_start: 0.5941 (OUTLIER) cc_final: 0.5155 (m) REVERT: B 189 MET cc_start: 0.8830 (tmm) cc_final: 0.8627 (tmm) REVERT: B 258 MET cc_start: 0.5997 (pmm) cc_final: 0.5710 (pmm) outliers start: 26 outliers final: 18 residues processed: 126 average time/residue: 0.0594 time to fit residues: 11.5574 Evaluate side-chains 122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain B residue 394 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.191963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133375 restraints weight = 10468.906| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.83 r_work: 0.3409 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7418 Z= 0.142 Angle : 0.651 10.497 10106 Z= 0.301 Chirality : 0.041 0.163 1165 Planarity : 0.004 0.045 1257 Dihedral : 3.859 23.218 1070 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.84 % Allowed : 28.00 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 1.53 (0.28), residues: 920 helix: 2.17 (0.23), residues: 538 sheet: 0.14 (0.72), residues: 62 loop : -0.85 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 207 TYR 0.042 0.002 TYR B 337 PHE 0.014 0.001 PHE A 542 TRP 0.028 0.001 TRP B 469 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7413) covalent geometry : angle 0.64951 (10092) SS BOND : bond 0.00357 ( 1) SS BOND : angle 1.55678 ( 2) hydrogen bonds : bond 0.03580 ( 430) hydrogen bonds : angle 3.82555 ( 1242) link_NAG-ASN : bond 0.00246 ( 4) link_NAG-ASN : angle 1.18271 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.17 seconds wall clock time: 41 minutes 10.64 seconds (2470.64 seconds total)