Starting phenix.real_space_refine on Fri Jul 19 09:18:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wns_37671/07_2024/8wns_37671.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wns_37671/07_2024/8wns_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wns_37671/07_2024/8wns_37671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wns_37671/07_2024/8wns_37671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wns_37671/07_2024/8wns_37671.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wns_37671/07_2024/8wns_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 Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 445": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.75, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.74 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: 2.01 Time building geometry restraints manager: 2.92 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: 98.81 - 105.85: 172 105.85 - 112.88: 4007 112.88 - 119.91: 2429 119.91 - 126.95: 3371 126.95 - 133.98: 113 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 2.520 nonbonded pdb=" O LYS A 417 " pdb=" OG1 THR A 421 " model vdw 2.215 2.440 nonbonded pdb=" O HIS A 266 " pdb=" OH TYR A 313 " model vdw 2.226 2.440 nonbonded pdb=" O SER A 582 " pdb=" OG SER A 582 " model vdw 2.255 2.440 nonbonded pdb=" NH1 ARG A 535 " pdb=" OD1 ASN B 153 " model vdw 2.259 2.520 ... (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 ========== 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: 0.720 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.030 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- 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 7413 Z= 0.213 Angle : 0.646 9.392 10092 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.828 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 106 average time/residue: 0.1429 time to fit residues: 22.3681 Evaluate side-chains 104 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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: 1.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.0670 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- 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 187 GLN ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7413 Z= 0.247 Angle : 0.607 7.640 10092 Z= 0.290 Chirality : 0.040 0.187 1165 Planarity : 0.004 0.043 1257 Dihedral : 4.339 54.447 1073 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.00 % Allowed : 26.58 % Favored : 69.42 % 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 (0.29), residues: 920 helix: 2.13 (0.23), residues: 537 sheet: 0.65 (0.77), residues: 57 loop : -0.76 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 469 HIS 0.004 0.001 HIS A 557 PHE 0.021 0.001 PHE B 442 TYR 0.017 0.001 TYR B 337 ARG 0.001 0.000 ARG A 525 *********************** 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 135 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6701 (mm) REVERT: A 360 PHE cc_start: 0.7777 (m-80) cc_final: 0.7501 (m-80) REVERT: B 145 TYR cc_start: 0.8361 (m-80) cc_final: 0.7599 (m-80) REVERT: B 304 VAL cc_start: 0.8136 (m) cc_final: 0.7650 (m) outliers start: 31 outliers final: 17 residues processed: 125 average time/residue: 0.1406 time to fit residues: 25.9892 Evaluate side-chains 116 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 595 ASP 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 394 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7413 Z= 0.172 Angle : 0.553 7.285 10092 Z= 0.265 Chirality : 0.038 0.174 1165 Planarity : 0.004 0.044 1257 Dihedral : 3.757 16.613 1070 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.13 % Allowed : 26.97 % Favored : 68.90 % 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: 1.76 (0.29), residues: 920 helix: 2.26 (0.23), residues: 538 sheet: 0.75 (0.77), residues: 57 loop : -0.66 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 469 HIS 0.002 0.000 HIS B 349 PHE 0.016 0.001 PHE A 542 TYR 0.016 0.001 TYR B 337 ARG 0.001 0.000 ARG B 470 *********************** 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 153 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8070 (t0) cc_final: 0.7610 (t0) REVERT: A 339 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6459 (mm) REVERT: A 360 PHE cc_start: 0.7742 (m-80) cc_final: 0.7428 (m-80) REVERT: B 92 CYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8326 (t) REVERT: B 145 TYR cc_start: 0.8446 (m-80) cc_final: 0.7610 (m-80) outliers start: 32 outliers final: 16 residues processed: 147 average time/residue: 0.1600 time to fit residues: 33.7404 Evaluate side-chains 121 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 323 GLN 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 398 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 106 ASP 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 62 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 0.0050 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7413 Z= 0.204 Angle : 0.577 8.365 10092 Z= 0.275 Chirality : 0.039 0.170 1165 Planarity : 0.004 0.045 1257 Dihedral : 3.772 17.119 1070 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.90 % Allowed : 26.45 % Favored : 68.65 % 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: 1.72 (0.29), residues: 920 helix: 2.23 (0.23), residues: 537 sheet: 0.81 (0.77), residues: 57 loop : -0.69 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 469 HIS 0.003 0.001 HIS A 557 PHE 0.036 0.002 PHE B 442 TYR 0.011 0.001 TYR B 337 ARG 0.002 0.000 ARG A 626 *********************** 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 145 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 107 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8085 (t0) cc_final: 0.7599 (t0) REVERT: A 339 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6530 (mm) REVERT: A 360 PHE cc_start: 0.7747 (m-80) cc_final: 0.7468 (m-80) REVERT: A 521 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8126 (tt) REVERT: B 92 CYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8519 (t) REVERT: B 128 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8770 (mm) REVERT: B 145 TYR cc_start: 0.8484 (m-80) cc_final: 0.7736 (m-80) REVERT: B 447 MET cc_start: 0.6675 (tpp) cc_final: 0.6040 (tpp) outliers start: 38 outliers final: 22 residues processed: 138 average time/residue: 0.1378 time to fit residues: 28.3110 Evaluate side-chains 127 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 325 ASP 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 398 ASP 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 475 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 595 ASP 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 106 ASP Chi-restraints excluded: chain B residue 128 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 485 HIS ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7413 Z= 0.294 Angle : 0.618 8.580 10092 Z= 0.297 Chirality : 0.041 0.175 1165 Planarity : 0.004 0.045 1257 Dihedral : 3.957 17.872 1070 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.81 % Allowed : 25.29 % Favored : 68.90 % 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: 1.59 (0.29), residues: 920 helix: 2.20 (0.23), residues: 536 sheet: 0.53 (0.72), residues: 62 loop : -0.83 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 469 HIS 0.010 0.001 HIS B 485 PHE 0.025 0.002 PHE B 442 TYR 0.027 0.002 TYR B 337 ARG 0.002 0.000 ARG A 604 *********************** 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 148 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 103 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8126 (t0) cc_final: 0.7648 (t0) REVERT: A 339 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6713 (mm) REVERT: A 360 PHE cc_start: 0.7744 (m-80) cc_final: 0.7438 (m-80) REVERT: A 521 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8228 (tt) REVERT: B 92 CYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8547 (t) REVERT: B 128 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8803 (mm) REVERT: B 258 MET cc_start: 0.5239 (pmm) cc_final: 0.4946 (pmm) outliers start: 45 outliers final: 29 residues processed: 138 average time/residue: 0.1339 time to fit residues: 27.0539 Evaluate side-chains 128 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 325 ASP 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 398 ASP 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 521 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 595 ASP 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 106 ASP Chi-restraints excluded: chain B residue 128 LEU 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 285 ILE 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 79 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 187 GLN ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7413 Z= 0.189 Angle : 0.590 8.308 10092 Z= 0.281 Chirality : 0.040 0.174 1165 Planarity : 0.004 0.044 1257 Dihedral : 3.900 22.749 1070 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.77 % Allowed : 26.97 % Favored : 68.26 % 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: 1.69 (0.29), residues: 920 helix: 2.27 (0.23), residues: 536 sheet: 0.78 (0.76), residues: 57 loop : -0.80 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 469 HIS 0.002 0.000 HIS A 557 PHE 0.018 0.001 PHE B 442 TYR 0.023 0.001 TYR B 337 ARG 0.003 0.000 ARG A 210 *********************** 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 141 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 104 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8108 (t0) cc_final: 0.7642 (t0) REVERT: A 339 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6510 (mm) REVERT: A 360 PHE cc_start: 0.7751 (m-80) cc_final: 0.7450 (m-80) REVERT: A 521 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8166 (tt) REVERT: B 92 CYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8562 (t) REVERT: B 258 MET cc_start: 0.5312 (pmm) cc_final: 0.5069 (pmm) REVERT: B 495 TYR cc_start: 0.7459 (t80) cc_final: 0.7174 (t80) outliers start: 37 outliers final: 24 residues processed: 132 average time/residue: 0.1353 time to fit residues: 26.5338 Evaluate side-chains 126 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 323 GLN 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 398 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 595 ASP 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 106 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 394 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 187 GLN B 213 HIS ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7413 Z= 0.228 Angle : 0.613 8.111 10092 Z= 0.291 Chirality : 0.041 0.223 1165 Planarity : 0.004 0.044 1257 Dihedral : 4.104 42.966 1070 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.32 % Allowed : 25.55 % Favored : 68.13 % 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: 1.64 (0.29), residues: 920 helix: 2.27 (0.23), residues: 537 sheet: 0.82 (0.74), residues: 57 loop : -0.92 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 469 HIS 0.004 0.001 HIS A 557 PHE 0.016 0.001 PHE A 542 TYR 0.022 0.002 TYR B 109 ARG 0.001 0.000 ARG A 227 *********************** 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 150 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 101 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8099 (t0) cc_final: 0.7669 (t0) REVERT: A 339 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6567 (mm) REVERT: A 360 PHE cc_start: 0.7743 (m-80) cc_final: 0.7438 (m-80) REVERT: A 521 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8227 (tt) REVERT: B 258 MET cc_start: 0.5352 (pmm) cc_final: 0.5122 (pmm) REVERT: B 431 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8344 (pp) REVERT: B 447 MET cc_start: 0.6691 (tpp) cc_final: 0.6026 (tpp) REVERT: B 495 TYR cc_start: 0.7479 (t80) cc_final: 0.7196 (t80) outliers start: 49 outliers final: 34 residues processed: 141 average time/residue: 0.1442 time to fit residues: 29.8981 Evaluate side-chains 135 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 290 ASP Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 325 ASP 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 398 ASP 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 521 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 598 LEU 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 106 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 LEU 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 285 ILE Chi-restraints excluded: chain B residue 304 VAL 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 Chi-restraints excluded: chain B residue 431 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7413 Z= 0.181 Angle : 0.590 8.152 10092 Z= 0.277 Chirality : 0.040 0.210 1165 Planarity : 0.004 0.043 1257 Dihedral : 3.872 33.256 1070 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.39 % Allowed : 27.35 % Favored : 68.26 % 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: 1.75 (0.29), residues: 920 helix: 2.38 (0.23), residues: 537 sheet: 0.82 (0.74), residues: 57 loop : -0.93 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 469 HIS 0.002 0.000 HIS A 557 PHE 0.016 0.001 PHE A 542 TYR 0.024 0.001 TYR B 109 ARG 0.002 0.000 ARG A 212 *********************** 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 141 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 107 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8084 (t0) cc_final: 0.7654 (t0) REVERT: A 339 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6551 (mm) REVERT: A 360 PHE cc_start: 0.7787 (m-80) cc_final: 0.7489 (m-80) REVERT: B 431 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8399 (pp) REVERT: B 447 MET cc_start: 0.6662 (tpp) cc_final: 0.5989 (tpp) outliers start: 34 outliers final: 29 residues processed: 134 average time/residue: 0.1425 time to fit residues: 28.0106 Evaluate side-chains 134 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 325 ASP 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 398 ASP 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 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 595 ASP 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 106 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 304 VAL 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 431 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 187 GLN ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7413 Z= 0.233 Angle : 0.631 9.327 10092 Z= 0.296 Chirality : 0.041 0.185 1165 Planarity : 0.004 0.044 1257 Dihedral : 3.904 29.875 1070 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.13 % Allowed : 27.74 % Favored : 68.13 % 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: 2.32 (0.23), residues: 537 sheet: 0.81 (0.74), residues: 57 loop : -1.04 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 469 HIS 0.004 0.001 HIS A 557 PHE 0.016 0.001 PHE A 542 TYR 0.018 0.001 TYR B 337 ARG 0.002 0.000 ARG A 227 *********************** 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 fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8081 (t0) cc_final: 0.7702 (t0) REVERT: A 339 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6623 (mm) REVERT: A 360 PHE cc_start: 0.7749 (m-80) cc_final: 0.7442 (m-80) REVERT: B 431 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8364 (pp) REVERT: B 447 MET cc_start: 0.6695 (tpp) cc_final: 0.6026 (tpp) outliers start: 32 outliers final: 29 residues processed: 126 average time/residue: 0.1354 time to fit residues: 25.4730 Evaluate side-chains 130 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 325 ASP 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 398 ASP 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 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 595 ASP 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 106 ASP Chi-restraints excluded: chain B residue 117 LEU 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 299 SER Chi-restraints excluded: chain B residue 304 VAL 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 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7413 Z= 0.228 Angle : 0.627 9.383 10092 Z= 0.294 Chirality : 0.041 0.191 1165 Planarity : 0.004 0.045 1257 Dihedral : 3.884 25.964 1070 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.13 % Allowed : 28.26 % Favored : 67.61 % 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: 1.62 (0.29), residues: 920 helix: 2.33 (0.23), residues: 537 sheet: 0.77 (0.74), residues: 57 loop : -1.09 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 469 HIS 0.004 0.001 HIS A 557 PHE 0.016 0.001 PHE A 542 TYR 0.018 0.001 TYR B 337 ARG 0.002 0.000 ARG A 227 ********************** 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 133 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.8081 (t0) cc_final: 0.7728 (t0) REVERT: A 339 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6585 (mm) REVERT: A 360 PHE cc_start: 0.7752 (m-80) cc_final: 0.7448 (m-80) REVERT: B 154 CYS cc_start: 0.5034 (OUTLIER) cc_final: 0.4685 (m) outliers start: 32 outliers final: 29 residues processed: 127 average time/residue: 0.1376 time to fit residues: 25.9735 Evaluate side-chains 130 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 290 ASP Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 325 ASP 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 398 ASP 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 521 LEU Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 595 ASP 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 106 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 324 LEU 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 66 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 0.0020 chunk 52 optimal weight: 8.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.192316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126357 restraints weight = 10318.145| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.70 r_work: 0.3457 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7413 Z= 0.168 Angle : 0.616 9.932 10092 Z= 0.284 Chirality : 0.039 0.176 1165 Planarity : 0.004 0.044 1257 Dihedral : 3.735 23.403 1070 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.13 % Allowed : 28.13 % Favored : 67.74 % 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: 1.66 (0.29), residues: 920 helix: 2.35 (0.23), residues: 537 sheet: 0.83 (0.74), residues: 57 loop : -1.07 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 469 HIS 0.002 0.000 HIS A 557 PHE 0.015 0.001 PHE A 542 TYR 0.019 0.001 TYR B 337 ARG 0.001 0.000 ARG A 563 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1758.50 seconds wall clock time: 32 minutes 23.71 seconds (1943.71 seconds total)