Starting phenix.real_space_refine on Sat Aug 3 06:37:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wns_37671/08_2024/8wns_37671.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wns_37671/08_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_37671/08_2024/8wns_37671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wns_37671/08_2024/8wns_37671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wns_37671/08_2024/8wns_37671.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wns_37671/08_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-5409/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: 4.54, per 1000 atoms: 0.63 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: 2.92 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: 0.93 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: 2.15 Time building geometry restraints manager: 3.21 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 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: 0.690 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.830 Find NCS groups from input model: 0.110 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- 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 : 0.689 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 106 average time/residue: 0.1465 time to fit residues: 22.8513 Evaluate side-chains 104 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7413 Z= 0.202 Angle : 0.607 8.006 10092 Z= 0.291 Chirality : 0.040 0.200 1165 Planarity : 0.004 0.042 1257 Dihedral : 4.350 55.910 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 *********************** 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 fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASN cc_start: 0.7997 (t0) cc_final: 0.7629 (t0) REVERT: A 339 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6693 (mm) REVERT: A 360 PHE cc_start: 0.7763 (m-80) cc_final: 0.7420 (m-80) REVERT: B 145 TYR cc_start: 0.8328 (m-80) cc_final: 0.7625 (m-80) outliers start: 27 outliers final: 14 residues processed: 129 average time/residue: 0.1525 time to fit residues: 28.3925 Evaluate side-chains 117 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 68 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.0020 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1135 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= 0.206 Angle : 0.573 7.507 10092 Z= 0.279 Chirality : 0.039 0.177 1165 Planarity : 0.004 0.044 1257 Dihedral : 3.880 16.700 1070 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.97 % Allowed : 26.97 % Favored : 70.06 % 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: 1.61 (0.28), residues: 920 helix: 2.16 (0.22), residues: 539 sheet: 0.43 (0.73), residues: 62 loop : -0.73 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 469 HIS 0.004 0.001 HIS B 349 PHE 0.016 0.001 PHE A 542 TYR 0.015 0.001 TYR B 337 ARG 0.005 0.000 ARG A 207 *********************** 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 137 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 317 ASN cc_start: 0.7930 (t0) cc_final: 0.7648 (t0) REVERT: A 339 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6665 (mm) REVERT: A 360 PHE cc_start: 0.7771 (m-80) cc_final: 0.7410 (m-80) REVERT: B 92 CYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8431 (t) REVERT: B 145 TYR cc_start: 0.8424 (m-80) cc_final: 0.7596 (m-80) outliers start: 23 outliers final: 12 residues processed: 129 average time/residue: 0.1427 time to fit residues: 27.0149 Evaluate side-chains 116 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 62 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1321 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= 0.226 Angle : 0.589 7.653 10092 Z= 0.284 Chirality : 0.040 0.171 1165 Planarity : 0.004 0.046 1257 Dihedral : 3.872 17.404 1070 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.13 % Allowed : 26.06 % 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: 1.57 (0.28), residues: 920 helix: 2.15 (0.22), residues: 539 sheet: 0.38 (0.73), residues: 62 loop : -0.78 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 469 HIS 0.011 0.001 HIS B 485 PHE 0.016 0.001 PHE A 542 TYR 0.029 0.002 TYR B 337 ARG 0.004 0.000 ARG A 207 *********************** 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 144 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 317 ASN cc_start: 0.7938 (t0) cc_final: 0.7699 (t0) REVERT: A 339 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6669 (mm) REVERT: A 360 PHE cc_start: 0.7741 (m-80) cc_final: 0.7398 (m-80) REVERT: B 92 CYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8501 (t) REVERT: B 145 TYR cc_start: 0.8493 (m-80) cc_final: 0.7731 (m-80) REVERT: B 495 TYR cc_start: 0.7432 (t80) cc_final: 0.7132 (t80) outliers start: 32 outliers final: 15 residues processed: 137 average time/residue: 0.1565 time to fit residues: 31.2759 Evaluate side-chains 119 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 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 49 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 44 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 213 HIS B 294 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7413 Z= 0.376 Angle : 0.665 7.807 10092 Z= 0.327 Chirality : 0.043 0.188 1165 Planarity : 0.004 0.046 1257 Dihedral : 4.250 22.539 1070 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.29 % Allowed : 24.90 % 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: 1.38 (0.28), residues: 920 helix: 2.03 (0.22), residues: 540 sheet: 0.15 (0.71), residues: 65 loop : -0.92 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.010 0.001 HIS B 68 PHE 0.041 0.002 PHE B 442 TYR 0.021 0.002 TYR B 337 ARG 0.005 0.000 ARG A 207 *********************** 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 140 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 99 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7010 (mm) REVERT: A 360 PHE cc_start: 0.7750 (m-80) cc_final: 0.7415 (m-80) REVERT: B 92 CYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8593 (t) outliers start: 41 outliers final: 27 residues processed: 128 average time/residue: 0.1389 time to fit residues: 26.8624 Evaluate side-chains 122 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 265 ILE 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 53 ILE 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 117 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 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: 0.0980 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 601 GLN B 284 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7413 Z= 0.188 Angle : 0.609 9.094 10092 Z= 0.292 Chirality : 0.040 0.175 1165 Planarity : 0.004 0.045 1257 Dihedral : 4.209 39.115 1070 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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 : 0.11 % 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: 1.57 (0.29), residues: 920 helix: 2.22 (0.23), residues: 534 sheet: 0.23 (0.74), residues: 62 loop : -0.84 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 469 HIS 0.012 0.001 HIS B 485 PHE 0.023 0.001 PHE B 442 TYR 0.023 0.002 TYR B 109 ARG 0.004 0.000 ARG A 207 *********************** 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 137 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6686 (mm) REVERT: A 360 PHE cc_start: 0.7738 (m-80) cc_final: 0.7405 (m-80) REVERT: B 92 CYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8534 (t) REVERT: B 258 MET cc_start: 0.5544 (pmm) cc_final: 0.5265 (pmm) REVERT: B 495 TYR cc_start: 0.7353 (t80) cc_final: 0.7076 (t80) outliers start: 32 outliers final: 12 residues processed: 129 average time/residue: 0.1598 time to fit residues: 30.0585 Evaluate side-chains 115 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 93 TYR Chi-restraints excluded: chain B residue 98 VAL 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 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: 4.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 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 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1838 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= 0.213 Angle : 0.620 8.867 10092 Z= 0.297 Chirality : 0.041 0.184 1165 Planarity : 0.004 0.046 1257 Dihedral : 4.089 32.886 1070 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.61 % Allowed : 27.61 % Favored : 68.77 % 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: 1.58 (0.29), residues: 920 helix: 2.21 (0.23), residues: 538 sheet: 0.19 (0.74), residues: 62 loop : -0.82 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 469 HIS 0.004 0.001 HIS B 68 PHE 0.016 0.001 PHE B 327 TYR 0.037 0.002 TYR B 337 ARG 0.004 0.000 ARG A 207 *********************** 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 135 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6723 (mm) REVERT: A 360 PHE cc_start: 0.7741 (m-80) cc_final: 0.7402 (m-80) REVERT: B 92 CYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8463 (t) REVERT: B 170 MET cc_start: 0.7334 (mtt) cc_final: 0.7098 (mtm) REVERT: B 258 MET cc_start: 0.5588 (pmm) cc_final: 0.5325 (pmm) REVERT: B 281 THR cc_start: 0.8609 (m) cc_final: 0.8209 (p) REVERT: B 431 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8372 (pp) REVERT: B 495 TYR cc_start: 0.7367 (t80) cc_final: 0.7095 (t80) outliers start: 28 outliers final: 19 residues processed: 129 average time/residue: 0.1397 time to fit residues: 26.5506 Evaluate side-chains 121 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 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 92 CYS Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 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 431 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 0.0370 chunk 76 optimal weight: 9.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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** B 485 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: 0.7488 moved from start: 0.1936 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= 0.191 Angle : 0.605 9.195 10092 Z= 0.289 Chirality : 0.041 0.178 1165 Planarity : 0.004 0.045 1257 Dihedral : 3.983 27.871 1070 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.13 % Allowed : 27.35 % Favored : 68.52 % 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: 2.26 (0.23), residues: 538 sheet: 0.26 (0.74), residues: 62 loop : -0.82 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 469 HIS 0.013 0.001 HIS B 485 PHE 0.016 0.001 PHE B 327 TYR 0.032 0.002 TYR B 337 ARG 0.004 0.000 ARG A 207 *********************** 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 139 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 339 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6665 (mm) REVERT: A 360 PHE cc_start: 0.7705 (m-80) cc_final: 0.7394 (m-80) REVERT: B 92 CYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8459 (t) REVERT: B 170 MET cc_start: 0.7293 (mtt) cc_final: 0.7062 (mtm) REVERT: B 258 MET cc_start: 0.5630 (pmm) cc_final: 0.5423 (pmm) REVERT: B 281 THR cc_start: 0.8554 (m) cc_final: 0.8165 (p) REVERT: B 447 MET cc_start: 0.6650 (tpp) cc_final: 0.5911 (tpp) outliers start: 32 outliers final: 20 residues processed: 136 average time/residue: 0.1410 time to fit residues: 28.3121 Evaluate side-chains 121 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 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 485 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** B 485 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7413 Z= 0.239 Angle : 0.633 9.790 10092 Z= 0.301 Chirality : 0.041 0.167 1165 Planarity : 0.004 0.045 1257 Dihedral : 3.991 26.011 1070 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.48 % Allowed : 27.87 % 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: 1.57 (0.29), residues: 920 helix: 2.22 (0.22), residues: 538 sheet: 0.23 (0.74), residues: 62 loop : -0.87 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 469 HIS 0.013 0.001 HIS B 485 PHE 0.023 0.001 PHE A 337 TYR 0.030 0.002 TYR B 337 ARG 0.006 0.000 ARG A 207 *********************** 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 124 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 339 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6636 (mm) REVERT: A 360 PHE cc_start: 0.7722 (m-80) cc_final: 0.7419 (m-80) REVERT: B 154 CYS cc_start: 0.5414 (OUTLIER) cc_final: 0.4775 (m) REVERT: B 170 MET cc_start: 0.7298 (mtt) cc_final: 0.7061 (mtm) REVERT: B 258 MET cc_start: 0.5669 (pmm) cc_final: 0.5453 (pmm) REVERT: B 281 THR cc_start: 0.8466 (m) cc_final: 0.8091 (p) REVERT: B 447 MET cc_start: 0.6643 (tpp) cc_final: 0.5907 (tpp) outliers start: 27 outliers final: 19 residues processed: 122 average time/residue: 0.1428 time to fit residues: 25.6785 Evaluate side-chains 117 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 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 259 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 485 HIS 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 41 optimal weight: 0.0040 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.0370 chunk 57 optimal weight: 0.1980 chunk 76 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 overall best weight: 0.3270 ------------------------------------------------------------------------------- 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** B 485 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2072 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= 0.173 Angle : 0.614 10.625 10092 Z= 0.290 Chirality : 0.040 0.165 1165 Planarity : 0.004 0.045 1257 Dihedral : 3.906 24.133 1070 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.97 % Allowed : 28.13 % 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: 1.60 (0.29), residues: 920 helix: 2.22 (0.22), residues: 539 sheet: 0.31 (0.73), residues: 62 loop : -0.85 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 469 HIS 0.014 0.001 HIS B 485 PHE 0.026 0.001 PHE A 337 TYR 0.030 0.001 TYR B 337 ARG 0.006 0.000 ARG A 207 ********************** 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 132 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6593 (mm) REVERT: A 360 PHE cc_start: 0.7746 (m-80) cc_final: 0.7436 (m-80) REVERT: B 154 CYS cc_start: 0.5462 (OUTLIER) cc_final: 0.4864 (m) REVERT: B 170 MET cc_start: 0.7287 (mtt) cc_final: 0.7056 (mtm) REVERT: B 281 THR cc_start: 0.8523 (m) cc_final: 0.8158 (p) REVERT: B 434 TRP cc_start: 0.7751 (t60) cc_final: 0.7370 (t60) REVERT: B 447 MET cc_start: 0.6609 (tpp) cc_final: 0.5887 (tpp) outliers start: 23 outliers final: 19 residues processed: 127 average time/residue: 0.1429 time to fit residues: 27.0056 Evaluate side-chains 116 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 93 TYR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 485 HIS Chi-restraints excluded: chain B residue 486 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.0366 > 50: distance: 1 - 16: 7.971 distance: 6 - 23: 28.040 distance: 10 - 30: 22.869 distance: 13 - 16: 11.672 distance: 14 - 38: 24.759 distance: 16 - 17: 4.600 distance: 17 - 18: 6.965 distance: 17 - 20: 20.963 distance: 18 - 19: 25.995 distance: 18 - 23: 28.644 distance: 19 - 46: 24.645 distance: 20 - 21: 10.064 distance: 20 - 22: 14.281 distance: 23 - 24: 39.341 distance: 24 - 25: 19.904 distance: 24 - 27: 39.529 distance: 25 - 26: 13.433 distance: 25 - 30: 24.999 distance: 26 - 53: 25.813 distance: 27 - 28: 28.191 distance: 27 - 29: 27.913 distance: 30 - 31: 18.417 distance: 31 - 32: 24.243 distance: 31 - 34: 24.711 distance: 32 - 33: 42.659 distance: 32 - 38: 13.357 distance: 34 - 35: 29.719 distance: 34 - 36: 28.235 distance: 35 - 37: 23.469 distance: 38 - 39: 36.975 distance: 39 - 40: 22.891 distance: 39 - 42: 3.441 distance: 40 - 41: 30.127 distance: 40 - 46: 33.926 distance: 42 - 43: 25.456 distance: 42 - 44: 17.483 distance: 43 - 45: 13.459 distance: 46 - 47: 13.369 distance: 47 - 48: 47.674 distance: 48 - 49: 3.315 distance: 48 - 53: 42.598 distance: 50 - 51: 26.657 distance: 50 - 52: 15.557 distance: 53 - 54: 36.428 distance: 54 - 55: 34.703 distance: 54 - 57: 18.705 distance: 55 - 56: 45.095 distance: 55 - 64: 41.731 distance: 57 - 58: 34.858 distance: 58 - 59: 31.576 distance: 59 - 60: 20.897 distance: 60 - 61: 14.061 distance: 61 - 62: 14.555 distance: 61 - 63: 13.942 distance: 64 - 65: 48.688 distance: 65 - 66: 42.470 distance: 65 - 68: 44.615 distance: 66 - 67: 26.543 distance: 66 - 69: 29.884 distance: 69 - 70: 28.224 distance: 69 - 75: 37.593 distance: 70 - 71: 29.967 distance: 70 - 73: 42.634 distance: 71 - 72: 40.613 distance: 71 - 76: 40.724 distance: 73 - 74: 21.788 distance: 74 - 75: 20.094 distance: 76 - 77: 19.300 distance: 77 - 78: 31.493 distance: 77 - 80: 35.400 distance: 78 - 79: 7.166 distance: 78 - 87: 25.210 distance: 80 - 81: 32.527 distance: 81 - 82: 9.856 distance: 82 - 83: 39.684 distance: 83 - 84: 33.770 distance: 84 - 85: 28.652 distance: 84 - 86: 16.092 distance: 87 - 88: 44.186 distance: 88 - 89: 31.740 distance: 88 - 91: 41.741 distance: 89 - 90: 48.345 distance: 89 - 93: 21.945 distance: 91 - 92: 33.280 distance: 92 - 123: 28.904