Starting phenix.real_space_refine on Mon Apr 28 08:39:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wns_37671/04_2025/8wns_37671.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wns_37671/04_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_37671/04_2025/8wns_37671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wns_37671/04_2025/8wns_37671.map" model { file = "/net/cci-nas-00/data/ceres_data/8wns_37671/04_2025/8wns_37671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wns_37671/04_2025/8wns_37671.cif" } resolution = 3.42 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= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.93, per 1000 atoms: 0.68 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: 1.84 Conformation dependent library (CDL) restraints added in 995.3 milliseconds 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: 0.71 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: 1.99 Time building geometry restraints manager: 2.17 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: 1.260 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.320 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 25.110 ------------------------------------------------------------------------------- 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 : 10.68 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 (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: 1.29 (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 TRP 0.037 0.001 TRP B 469 HIS 0.004 0.001 HIS B 68 PHE 0.015 0.001 PHE A 542 TYR 0.033 0.001 TYR B 337 ARG 0.002 0.000 ARG A 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 4) link_NAG-ASN : angle 1.18693 ( 12) hydrogen bonds : bond 0.16297 ( 430) hydrogen bonds : angle 5.83908 ( 1242) SS BOND : bond 0.00099 ( 1) SS BOND : angle 1.19469 ( 2) covalent geometry : bond 0.00326 ( 7413) covalent geometry : angle 0.64647 (10092) *********************** 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 : 0.728 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 106 average time/residue: 0.1407 time to fit residues: 22.6332 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 : 0.765 ------------------------------------------------------------------------------- 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 76 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 358 HIS ** 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 = 0.4384 r_free = 0.4384 target = 0.188606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.130472 restraints weight = 10371.434| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.83 r_work: 0.3387 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.0839 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= 0.138 Angle : 0.609 7.978 10106 Z= 0.292 Chirality : 0.040 0.200 1165 Planarity : 0.004 0.042 1257 Dihedral : 4.349 55.860 1073 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.48 % Allowed : 25.94 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.28), residues: 920 helix: 2.09 (0.22), residues: 539 sheet: 0.45 (0.72), residues: 62 loop : -0.69 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 469 HIS 0.002 0.001 HIS A 557 PHE 0.021 0.001 PHE B 442 TYR 0.020 0.001 TYR B 337 ARG 0.003 0.000 ARG A 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 4) link_NAG-ASN : angle 1.39687 ( 12) hydrogen bonds : bond 0.04109 ( 430) hydrogen bonds : angle 4.26156 ( 1242) SS BOND : bond 0.00357 ( 1) SS BOND : angle 1.71655 ( 2) covalent geometry : bond 0.00307 ( 7413) covalent geometry : angle 0.60715 (10092) *********************** 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 137 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8352 (t0) cc_final: 0.7810 (t0) REVERT: A 339 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6511 (mm) REVERT: A 360 PHE cc_start: 0.7872 (m-80) cc_final: 0.7528 (m-80) REVERT: B 145 TYR cc_start: 0.8556 (m-80) cc_final: 0.7923 (m-80) outliers start: 27 outliers final: 14 residues processed: 129 average time/residue: 0.2051 time to fit residues: 38.3950 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 : 1.623 ------------------------------------------------------------------------------- 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 45 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 9 optimal weight: 0.2980 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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** A 620 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 = 0.4370 r_free = 0.4370 target = 0.187358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.121918 restraints weight = 10463.051| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.83 r_work: 0.3371 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7418 Z= 0.152 Angle : 0.585 7.541 10106 Z= 0.285 Chirality : 0.040 0.176 1165 Planarity : 0.004 0.044 1257 Dihedral : 3.931 16.884 1070 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.23 % Allowed : 26.97 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.28), residues: 920 helix: 2.13 (0.22), residues: 539 sheet: 0.39 (0.73), residues: 62 loop : -0.77 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 469 HIS 0.003 0.001 HIS A 557 PHE 0.016 0.001 PHE A 542 TYR 0.016 0.002 TYR B 337 ARG 0.006 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 4) link_NAG-ASN : angle 1.40027 ( 12) hydrogen bonds : bond 0.03993 ( 430) hydrogen bonds : angle 4.10030 ( 1242) SS BOND : bond 0.00247 ( 1) SS BOND : angle 1.48297 ( 2) covalent geometry : bond 0.00358 ( 7413) covalent geometry : angle 0.58294 (10092) *********************** 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 136 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8358 (t0) cc_final: 0.7779 (t0) REVERT: A 339 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6461 (mm) REVERT: A 360 PHE cc_start: 0.7876 (m-80) cc_final: 0.7563 (m-80) REVERT: B 92 CYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8453 (t) REVERT: B 145 TYR cc_start: 0.8672 (m-80) cc_final: 0.7938 (m-80) REVERT: B 442 PHE cc_start: 0.7959 (m-80) cc_final: 0.7673 (m-80) outliers start: 25 outliers final: 12 residues processed: 128 average time/residue: 0.1802 time to fit residues: 33.6127 Evaluate side-chains 116 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 464 THR 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 B residue 92 CYS Chi-restraints excluded: chain B residue 240 GLN 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 407 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.197628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.152397 restraints weight = 10625.916| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 3.52 r_work: 0.3598 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7418 Z= 0.136 Angle : 0.583 7.314 10106 Z= 0.281 Chirality : 0.040 0.172 1165 Planarity : 0.004 0.046 1257 Dihedral : 3.861 17.247 1070 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.52 % Allowed : 25.16 % 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 (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: 1.58 (0.28), residues: 920 helix: 2.15 (0.22), residues: 539 sheet: 0.36 (0.73), residues: 62 loop : -0.76 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 469 HIS 0.009 0.001 HIS B 485 PHE 0.016 0.001 PHE A 542 TYR 0.031 0.002 TYR B 337 ARG 0.004 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 4) link_NAG-ASN : angle 1.28950 ( 12) hydrogen bonds : bond 0.03739 ( 430) hydrogen bonds : angle 3.99363 ( 1242) SS BOND : bond 0.00104 ( 1) SS BOND : angle 1.33058 ( 2) covalent geometry : bond 0.00314 ( 7413) covalent geometry : angle 0.58131 (10092) *********************** 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 153 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8234 (t0) cc_final: 0.7805 (t0) REVERT: A 339 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6587 (mm) REVERT: A 360 PHE cc_start: 0.7904 (m-80) cc_final: 0.7539 (m-80) REVERT: B 92 CYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8372 (t) REVERT: B 145 TYR cc_start: 0.8779 (m-80) cc_final: 0.8094 (m-80) REVERT: B 442 PHE cc_start: 0.7607 (m-80) cc_final: 0.7307 (m-80) REVERT: B 495 TYR cc_start: 0.7484 (t80) cc_final: 0.7173 (t80) outliers start: 35 outliers final: 15 residues processed: 144 average time/residue: 0.2139 time to fit residues: 46.9171 Evaluate side-chains 122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 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 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 B residue 92 CYS 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 324 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 0.0370 chunk 21 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 601 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 HIS ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.193841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.130063 restraints weight = 10345.951| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 4.24 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7418 Z= 0.128 Angle : 0.585 7.874 10106 Z= 0.282 Chirality : 0.039 0.168 1165 Planarity : 0.004 0.047 1257 Dihedral : 3.897 19.238 1070 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.13 % Allowed : 25.94 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.28), residues: 920 helix: 2.19 (0.22), residues: 534 sheet: 0.34 (0.73), residues: 62 loop : -0.78 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 469 HIS 0.011 0.001 HIS B 485 PHE 0.016 0.001 PHE A 542 TYR 0.021 0.001 TYR B 337 ARG 0.006 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 4) link_NAG-ASN : angle 1.23304 ( 12) hydrogen bonds : bond 0.03648 ( 430) hydrogen bonds : angle 3.91024 ( 1242) SS BOND : bond 0.00053 ( 1) SS BOND : angle 1.99649 ( 2) covalent geometry : bond 0.00293 ( 7413) covalent geometry : angle 0.58282 (10092) *********************** 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 142 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8354 (t0) cc_final: 0.7912 (t0) REVERT: A 339 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6522 (mm) REVERT: A 360 PHE cc_start: 0.7905 (m-80) cc_final: 0.7529 (m-80) REVERT: B 92 CYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8520 (t) REVERT: B 128 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 145 TYR cc_start: 0.8494 (m-80) cc_final: 0.7789 (m-80) REVERT: B 442 PHE cc_start: 0.7861 (m-80) cc_final: 0.7610 (m-80) REVERT: B 447 MET cc_start: 0.6473 (tpp) cc_final: 0.5804 (tpp) REVERT: B 495 TYR cc_start: 0.7556 (t80) cc_final: 0.7226 (t80) outliers start: 32 outliers final: 19 residues processed: 135 average time/residue: 0.1293 time to fit residues: 26.3876 Evaluate side-chains 123 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 343 VAL 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 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 B residue 81 LEU Chi-restraints excluded: chain B residue 92 CYS 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 394 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 84 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 213 HIS B 284 ASN ** 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 = 0.4430 r_free = 0.4430 target = 0.191756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.130711 restraints weight = 10403.002| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.75 r_work: 0.3451 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7418 Z= 0.129 Angle : 0.598 8.906 10106 Z= 0.288 Chirality : 0.040 0.207 1165 Planarity : 0.004 0.046 1257 Dihedral : 4.089 40.473 1070 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.39 % Allowed : 25.68 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.63 (0.28), residues: 920 helix: 2.23 (0.23), residues: 534 sheet: 0.33 (0.74), residues: 62 loop : -0.77 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 469 HIS 0.003 0.001 HIS B 68 PHE 0.019 0.001 PHE A 337 TYR 0.038 0.002 TYR B 337 ARG 0.005 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 4) link_NAG-ASN : angle 1.22591 ( 12) hydrogen bonds : bond 0.03597 ( 430) hydrogen bonds : angle 3.88647 ( 1242) SS BOND : bond 0.00700 ( 1) SS BOND : angle 3.40344 ( 2) covalent geometry : bond 0.00297 ( 7413) covalent geometry : angle 0.59545 (10092) *********************** 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 139 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8301 (t0) cc_final: 0.7853 (t0) REVERT: A 339 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6397 (mm) REVERT: A 360 PHE cc_start: 0.7837 (m-80) cc_final: 0.7529 (m-80) REVERT: B 92 CYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8345 (t) REVERT: B 145 TYR cc_start: 0.8736 (m-80) cc_final: 0.8110 (m-80) REVERT: B 258 MET cc_start: 0.5626 (pmm) cc_final: 0.5197 (pmm) REVERT: B 281 THR cc_start: 0.8604 (m) cc_final: 0.8265 (p) REVERT: B 442 PHE cc_start: 0.7997 (m-80) cc_final: 0.7686 (m-80) REVERT: B 495 TYR cc_start: 0.7519 (t80) cc_final: 0.7259 (t80) outliers start: 34 outliers final: 22 residues processed: 133 average time/residue: 0.2049 time to fit residues: 41.1569 Evaluate side-chains 126 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 343 VAL 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 B residue 81 LEU Chi-restraints excluded: chain B residue 92 CYS 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 259 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 Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 53 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.186623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124215 restraints weight = 10518.676| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.86 r_work: 0.3340 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7418 Z= 0.271 Angle : 0.708 8.599 10106 Z= 0.344 Chirality : 0.044 0.183 1165 Planarity : 0.004 0.048 1257 Dihedral : 4.399 36.078 1070 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.16 % Allowed : 25.03 % 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 (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: 1.39 (0.28), residues: 920 helix: 2.07 (0.22), residues: 539 sheet: 0.06 (0.71), residues: 65 loop : -0.95 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 469 HIS 0.007 0.001 HIS A 557 PHE 0.029 0.002 PHE A 524 TYR 0.028 0.002 TYR B 337 ARG 0.004 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 4) link_NAG-ASN : angle 1.50518 ( 12) hydrogen bonds : bond 0.04489 ( 430) hydrogen bonds : angle 4.22934 ( 1242) SS BOND : bond 0.00415 ( 1) SS BOND : angle 3.44952 ( 2) covalent geometry : bond 0.00652 ( 7413) covalent geometry : angle 0.70538 (10092) *********************** 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 138 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8411 (t0) cc_final: 0.7929 (t0) REVERT: A 339 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6849 (mm) REVERT: B 258 MET cc_start: 0.6126 (pmm) cc_final: 0.5797 (pmm) REVERT: B 431 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8568 (pp) REVERT: B 442 PHE cc_start: 0.8071 (m-80) cc_final: 0.7717 (m-80) outliers start: 40 outliers final: 27 residues processed: 128 average time/residue: 0.2146 time to fit residues: 39.9538 Evaluate side-chains 122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 327 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 377 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 429 ASN 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 542 PHE Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 437 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 77 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 358 HIS ** 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 = 0.4418 r_free = 0.4418 target = 0.190731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.125481 restraints weight = 10522.689| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.27 r_work: 0.3438 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7418 Z= 0.136 Angle : 0.634 8.443 10106 Z= 0.301 Chirality : 0.042 0.193 1165 Planarity : 0.004 0.046 1257 Dihedral : 4.143 29.801 1070 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.74 % Allowed : 27.23 % 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 (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: 1.55 (0.28), residues: 920 helix: 2.21 (0.22), residues: 538 sheet: 0.23 (0.74), residues: 62 loop : -0.89 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 469 HIS 0.003 0.001 HIS B 68 PHE 0.017 0.001 PHE B 327 TYR 0.043 0.002 TYR B 337 ARG 0.004 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 4) link_NAG-ASN : angle 1.29784 ( 12) hydrogen bonds : bond 0.03810 ( 430) hydrogen bonds : angle 3.97093 ( 1242) SS BOND : bond 0.00710 ( 1) SS BOND : angle 1.79569 ( 2) covalent geometry : bond 0.00314 ( 7413) covalent geometry : angle 0.63283 (10092) *********************** 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 133 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8348 (t0) cc_final: 0.7930 (t0) REVERT: A 339 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6520 (mm) REVERT: A 360 PHE cc_start: 0.7930 (m-80) cc_final: 0.7570 (m-80) REVERT: A 575 LEU cc_start: 0.7891 (mp) cc_final: 0.7672 (mp) REVERT: B 170 MET cc_start: 0.7860 (mtt) cc_final: 0.7593 (mtm) REVERT: B 189 MET cc_start: 0.8802 (tmm) cc_final: 0.8595 (tmm) REVERT: B 258 MET cc_start: 0.6001 (pmm) cc_final: 0.5770 (pmm) REVERT: B 281 THR cc_start: 0.8549 (m) cc_final: 0.8189 (p) REVERT: B 442 PHE cc_start: 0.7803 (m-80) cc_final: 0.7495 (m-80) REVERT: B 495 TYR cc_start: 0.7643 (t80) cc_final: 0.7429 (t80) outliers start: 29 outliers final: 21 residues processed: 130 average time/residue: 0.1372 time to fit residues: 26.9368 Evaluate side-chains 127 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 339 LEU Chi-restraints excluded: chain A residue 343 VAL 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 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 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 259 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 Chi-restraints excluded: chain B residue 477 HIS 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 12 optimal weight: 0.0980 chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 0.0370 chunk 28 optimal weight: 0.5980 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 358 HIS ** 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 = 0.4422 r_free = 0.4422 target = 0.191340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.132484 restraints weight = 10546.743| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 3.70 r_work: 0.3432 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2063 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= 0.129 Angle : 0.626 10.065 10106 Z= 0.294 Chirality : 0.041 0.170 1165 Planarity : 0.004 0.046 1257 Dihedral : 4.009 26.144 1070 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.10 % Allowed : 27.35 % 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 (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: 1.63 (0.29), residues: 920 helix: 2.27 (0.23), residues: 538 sheet: 0.28 (0.74), residues: 62 loop : -0.87 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 469 HIS 0.003 0.001 HIS B 68 PHE 0.016 0.001 PHE B 327 TYR 0.033 0.002 TYR B 337 ARG 0.004 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 4) link_NAG-ASN : angle 1.25645 ( 12) hydrogen bonds : bond 0.03600 ( 430) hydrogen bonds : angle 3.88035 ( 1242) SS BOND : bond 0.00491 ( 1) SS BOND : angle 1.56650 ( 2) covalent geometry : bond 0.00299 ( 7413) covalent geometry : angle 0.62497 (10092) *********************** 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: 24 poor density : 107 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8338 (t0) cc_final: 0.7921 (t0) REVERT: A 339 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6470 (mm) REVERT: A 360 PHE cc_start: 0.7874 (m-80) cc_final: 0.7554 (m-80) REVERT: A 575 LEU cc_start: 0.7868 (mp) cc_final: 0.7638 (mp) REVERT: B 154 CYS cc_start: 0.6366 (OUTLIER) cc_final: 0.5364 (m) REVERT: B 170 MET cc_start: 0.7904 (mtt) cc_final: 0.7582 (mtm) REVERT: B 258 MET cc_start: 0.6083 (pmm) cc_final: 0.5868 (pmm) REVERT: B 281 THR cc_start: 0.8497 (m) cc_final: 0.8152 (p) REVERT: B 442 PHE cc_start: 0.7824 (m-80) cc_final: 0.7543 (m-80) REVERT: B 447 MET cc_start: 0.6635 (tpp) cc_final: 0.5953 (tpp) outliers start: 24 outliers final: 19 residues processed: 129 average time/residue: 0.1384 time to fit residues: 27.1431 Evaluate side-chains 121 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 339 LEU Chi-restraints excluded: chain A residue 343 VAL 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 489 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 81 LEU 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 259 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 Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 14 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 358 HIS ** 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 = 0.4431 r_free = 0.4431 target = 0.192183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128479 restraints weight = 10621.945| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.85 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7418 Z= 0.124 Angle : 0.641 10.745 10106 Z= 0.300 Chirality : 0.040 0.166 1165 Planarity : 0.004 0.045 1257 Dihedral : 3.920 23.933 1070 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.58 % Allowed : 27.87 % 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 (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: 1.64 (0.29), residues: 920 helix: 2.28 (0.23), residues: 538 sheet: 0.38 (0.74), residues: 62 loop : -0.89 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 469 HIS 0.003 0.001 HIS B 68 PHE 0.016 0.001 PHE B 327 TYR 0.015 0.001 TYR B 109 ARG 0.004 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 4) link_NAG-ASN : angle 1.16894 ( 12) hydrogen bonds : bond 0.03525 ( 430) hydrogen bonds : angle 3.85987 ( 1242) SS BOND : bond 0.00407 ( 1) SS BOND : angle 1.47407 ( 2) covalent geometry : bond 0.00286 ( 7413) covalent geometry : angle 0.64004 (10092) ********************** 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 124 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8394 (t0) cc_final: 0.7982 (t0) REVERT: A 339 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6439 (mm) REVERT: A 360 PHE cc_start: 0.7818 (m-80) cc_final: 0.7485 (m-80) REVERT: A 575 LEU cc_start: 0.7848 (mp) cc_final: 0.7604 (mp) REVERT: B 43 LEU cc_start: 0.8051 (mm) cc_final: 0.7533 (tp) REVERT: B 154 CYS cc_start: 0.5989 (OUTLIER) cc_final: 0.5162 (m) REVERT: B 170 MET cc_start: 0.7382 (mtt) cc_final: 0.7123 (mtm) REVERT: B 281 THR cc_start: 0.8525 (m) cc_final: 0.8155 (p) REVERT: B 447 MET cc_start: 0.6583 (tpp) cc_final: 0.5828 (tpp) REVERT: B 495 TYR cc_start: 0.7777 (t80) cc_final: 0.7542 (t80) outliers start: 20 outliers final: 15 residues processed: 122 average time/residue: 0.1410 time to fit residues: 25.7938 Evaluate side-chains 117 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 339 LEU Chi-restraints excluded: chain A residue 343 VAL 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 489 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 81 LEU 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 341 CYS Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 358 HIS ** 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 = 0.4474 r_free = 0.4474 target = 0.195615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.136907 restraints weight = 10398.985| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.63 r_work: 0.3526 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7418 Z= 0.170 Angle : 0.666 10.861 10106 Z= 0.315 Chirality : 0.042 0.170 1165 Planarity : 0.004 0.045 1257 Dihedral : 4.024 23.192 1070 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.10 % Allowed : 27.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.28), residues: 920 helix: 2.23 (0.22), residues: 539 sheet: 0.25 (0.73), residues: 62 loop : -0.98 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 469 HIS 0.005 0.001 HIS A 557 PHE 0.019 0.001 PHE B 327 TYR 0.015 0.002 TYR B 337 ARG 0.004 0.000 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 4) link_NAG-ASN : angle 1.23988 ( 12) hydrogen bonds : bond 0.03831 ( 430) hydrogen bonds : angle 3.94428 ( 1242) SS BOND : bond 0.00249 ( 1) SS BOND : angle 1.76854 ( 2) covalent geometry : bond 0.00410 ( 7413) covalent geometry : angle 0.66461 (10092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5350.70 seconds wall clock time: 97 minutes 15.84 seconds (5835.84 seconds total)