Starting phenix.real_space_refine on Fri Jul 25 10:30:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0w_37983/07_2025/8x0w_37983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0w_37983/07_2025/8x0w_37983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x0w_37983/07_2025/8x0w_37983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0w_37983/07_2025/8x0w_37983.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0w_37983/07_2025/8x0w_37983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0w_37983/07_2025/8x0w_37983.cif" } resolution = 3.1 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= 0.033 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 27 5.16 5 C 4813 2.51 5 N 1189 2.21 5 O 1339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7368 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3661 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 22, 'TRANS': 447} Chain: "B" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3586 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 4.64, per 1000 atoms: 0.63 Number of scatterers: 7368 At special positions: 0 Unit cell: (93.195, 78.66, 135.09, 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 27 16.00 O 1339 8.00 N 1189 7.00 C 4813 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 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 984.2 milliseconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 60.6% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 207 removed outlier: 3.655A pdb=" N VAL A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.884A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.605A pdb=" N GLY A 244 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 287 through 302 Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.718A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 356 through 372 removed outlier: 4.250A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.610A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 505 through 508 removed outlier: 3.713A pdb=" N MET A 508 " --> pdb=" O SER A 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 509 through 514 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 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 80 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 81 through 110 Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.878A pdb=" N ILE B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 157 removed outlier: 3.782A pdb=" N SER B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TYR B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 189 removed outlier: 3.542A pdb=" N ALA B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 221 Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.534A pdb=" N ILE B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 269 through 298 Proline residue: B 275 - end of helix Proline residue: B 283 - end of helix removed outlier: 3.599A pdb=" N PHE B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 325 through 355 removed outlier: 3.599A pdb=" N VAL B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 344 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 393 through 398 removed outlier: 4.167A pdb=" N ASN B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 422 removed outlier: 3.748A pdb=" N VAL B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 453 removed outlier: 3.811A pdb=" N VAL B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 removed outlier: 4.891A pdb=" N GLY B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 476 removed outlier: 4.651A pdb=" N VAL B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 501 removed outlier: 3.838A pdb=" N LEU B 486 " --> pdb=" O PRO B 482 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.452A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ARG A 349 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR A 226 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 225 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP A 434 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N SER A 468 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 543 through 544 removed outlier: 3.569A pdb=" N HIS A 543 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 627 " --> pdb=" O ARG A 563 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 567 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 594 393 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2279 1.34 - 1.46: 1787 1.46 - 1.58: 3442 1.58 - 1.70: 0 1.70 - 1.81: 40 Bond restraints: 7548 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C LEU A 584 " pdb=" N PRO A 585 " ideal model delta sigma weight residual 1.333 1.354 -0.021 1.01e-02 9.80e+03 4.16e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.54e+00 ... (remaining 7543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 10094 1.95 - 3.90: 147 3.90 - 5.85: 30 5.85 - 7.80: 6 7.80 - 9.75: 2 Bond angle restraints: 10279 Sorted by residual: angle pdb=" CA ARG A 614 " pdb=" CB ARG A 614 " pdb=" CG ARG A 614 " ideal model delta sigma weight residual 114.10 120.35 -6.25 2.00e+00 2.50e-01 9.75e+00 angle pdb=" CA LEU B 137 " pdb=" CB LEU B 137 " pdb=" CG LEU B 137 " ideal model delta sigma weight residual 116.30 126.05 -9.75 3.50e+00 8.16e-02 7.76e+00 angle pdb=" CA LEU B 466 " pdb=" CB LEU B 466 " pdb=" CG LEU B 466 " ideal model delta sigma weight residual 116.30 126.00 -9.70 3.50e+00 8.16e-02 7.69e+00 angle pdb=" C ILE B 59 " pdb=" CA ILE B 59 " pdb=" CB ILE B 59 " ideal model delta sigma weight residual 111.97 108.47 3.50 1.28e+00 6.10e-01 7.47e+00 angle pdb=" C SER A 321 " pdb=" CA SER A 321 " pdb=" CB SER A 321 " ideal model delta sigma weight residual 110.42 115.75 -5.33 1.99e+00 2.53e-01 7.18e+00 ... (remaining 10274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.02: 4136 25.02 - 50.04: 298 50.04 - 75.06: 24 75.06 - 100.08: 40 100.08 - 125.11: 29 Dihedral angle restraints: 4527 sinusoidal: 1848 harmonic: 2679 Sorted by residual: dihedral pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " pdb=" C5 NAG F 1 " ideal model delta sinusoidal sigma weight residual -62.96 62.15 -125.11 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " pdb=" C5 NAG D 2 " ideal model delta sinusoidal sigma weight residual -62.96 60.92 -123.88 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" N2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sinusoidal sigma weight residual -178.19 -60.85 -117.34 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 4524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1112 0.068 - 0.136: 99 0.136 - 0.204: 3 0.204 - 0.272: 1 0.272 - 0.340: 1 Chirality restraints: 1216 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 425 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 444 " pdb=" CB LEU B 444 " pdb=" CD1 LEU B 444 " pdb=" CD2 LEU B 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 1213 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 71 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO B 72 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 503 " -0.023 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO B 504 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 504 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 504 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 481 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO B 482 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 482 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 482 " -0.019 5.00e-02 4.00e+02 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1345 2.76 - 3.30: 7398 3.30 - 3.83: 12726 3.83 - 4.37: 13445 4.37 - 4.90: 23495 Nonbonded interactions: 58409 Sorted by model distance: nonbonded pdb=" O GLY B 67 " pdb=" OG1 THR B 71 " model vdw 2.229 3.040 nonbonded pdb=" O ILE B 139 " pdb=" OG SER B 143 " model vdw 2.308 3.040 nonbonded pdb=" OH TYR A 469 " pdb=" O PRO A 488 " model vdw 2.312 3.040 nonbonded pdb=" O ASP A 272 " pdb=" OG1 THR A 276 " model vdw 2.326 3.040 nonbonded pdb=" OD1 ASP A 271 " pdb=" ND2 ASN A 312 " model vdw 2.327 3.120 ... (remaining 58404 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.950 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: 19.740 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 0.075 7557 Z= 0.155 Angle : 0.624 10.879 10305 Z= 0.297 Chirality : 0.040 0.340 1216 Planarity : 0.003 0.050 1272 Dihedral : 21.595 125.106 2802 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.51 % Allowed : 13.69 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.29), residues: 930 helix: 2.32 (0.24), residues: 495 sheet: -0.35 (0.63), residues: 63 loop : -0.81 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 405 HIS 0.004 0.001 HIS B 367 PHE 0.015 0.001 PHE B 233 TYR 0.005 0.001 TYR B 289 ARG 0.001 0.000 ARG A 227 Details of bonding type rmsd link_NAG-ASN : bond 0.01042 ( 4) link_NAG-ASN : angle 4.15866 ( 12) link_BETA1-4 : bond 0.00607 ( 4) link_BETA1-4 : angle 1.73521 ( 12) hydrogen bonds : bond 0.13941 ( 393) hydrogen bonds : angle 5.18194 ( 1134) SS BOND : bond 0.00141 ( 1) SS BOND : angle 1.08288 ( 2) covalent geometry : bond 0.00304 ( 7548) covalent geometry : angle 0.60492 (10279) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 MET cc_start: 0.9126 (mmp) cc_final: 0.8164 (ppp) outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 0.1600 time to fit residues: 13.9007 Evaluate side-chains 50 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 233 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.0060 chunk 70 optimal weight: 0.0170 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.6436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.068885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047772 restraints weight = 28021.647| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 4.74 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7557 Z= 0.110 Angle : 0.645 11.461 10305 Z= 0.292 Chirality : 0.043 0.318 1216 Planarity : 0.004 0.052 1272 Dihedral : 20.620 116.664 1162 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.65 % Allowed : 13.69 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 930 helix: 2.47 (0.24), residues: 499 sheet: -0.45 (0.60), residues: 63 loop : -0.78 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 417 HIS 0.005 0.001 HIS B 367 PHE 0.013 0.001 PHE A 627 TYR 0.017 0.001 TYR A 423 ARG 0.002 0.000 ARG A 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00926 ( 4) link_NAG-ASN : angle 4.06586 ( 12) link_BETA1-4 : bond 0.00464 ( 4) link_BETA1-4 : angle 3.59714 ( 12) hydrogen bonds : bond 0.03552 ( 393) hydrogen bonds : angle 4.18272 ( 1134) SS BOND : bond 0.00690 ( 1) SS BOND : angle 3.89292 ( 2) covalent geometry : bond 0.00229 ( 7548) covalent geometry : angle 0.61572 (10279) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8903 (tt) REVERT: A 423 TYR cc_start: 0.9597 (t80) cc_final: 0.9374 (t80) REVERT: A 485 MET cc_start: 0.9070 (mmp) cc_final: 0.8477 (ppp) REVERT: B 365 MET cc_start: 0.9130 (tpp) cc_final: 0.8268 (mmt) REVERT: B 466 LEU cc_start: 0.9322 (tt) cc_final: 0.9114 (mm) outliers start: 13 outliers final: 4 residues processed: 65 average time/residue: 0.1477 time to fit residues: 14.6944 Evaluate side-chains 52 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 446 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 7 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 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 = 0.3344 r_free = 0.3344 target = 0.064941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.043325 restraints weight = 28919.318| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 4.73 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7557 Z= 0.245 Angle : 0.730 11.265 10305 Z= 0.338 Chirality : 0.045 0.334 1216 Planarity : 0.004 0.047 1272 Dihedral : 18.152 116.732 1160 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.53 % Allowed : 14.83 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.29), residues: 930 helix: 2.47 (0.24), residues: 494 sheet: -0.70 (0.60), residues: 63 loop : -0.85 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 89 HIS 0.006 0.002 HIS B 367 PHE 0.017 0.002 PHE A 524 TYR 0.014 0.002 TYR A 423 ARG 0.005 0.001 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00928 ( 4) link_NAG-ASN : angle 3.98099 ( 12) link_BETA1-4 : bond 0.00983 ( 4) link_BETA1-4 : angle 3.94401 ( 12) hydrogen bonds : bond 0.04884 ( 393) hydrogen bonds : angle 4.43209 ( 1134) SS BOND : bond 0.00498 ( 1) SS BOND : angle 3.27000 ( 2) covalent geometry : bond 0.00559 ( 7548) covalent geometry : angle 0.70432 (10279) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 289 GLU cc_start: 0.9454 (pm20) cc_final: 0.9254 (pm20) REVERT: A 485 MET cc_start: 0.9155 (mmt) cc_final: 0.8200 (ppp) outliers start: 20 outliers final: 10 residues processed: 61 average time/residue: 0.1410 time to fit residues: 13.3872 Evaluate side-chains 51 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 386 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 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 = 0.3361 r_free = 0.3361 target = 0.065701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.044506 restraints weight = 28530.559| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.67 r_work: 0.2611 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7557 Z= 0.146 Angle : 0.680 11.255 10305 Z= 0.300 Chirality : 0.042 0.320 1216 Planarity : 0.004 0.049 1272 Dihedral : 16.516 117.261 1158 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.90 % Allowed : 16.48 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 930 helix: 2.55 (0.24), residues: 496 sheet: -0.81 (0.60), residues: 63 loop : -0.80 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 405 HIS 0.005 0.001 HIS B 367 PHE 0.014 0.001 PHE B 233 TYR 0.017 0.001 TYR A 251 ARG 0.002 0.000 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00941 ( 4) link_NAG-ASN : angle 4.01229 ( 12) link_BETA1-4 : bond 0.00844 ( 4) link_BETA1-4 : angle 4.46119 ( 12) hydrogen bonds : bond 0.04171 ( 393) hydrogen bonds : angle 4.22810 ( 1134) SS BOND : bond 0.00494 ( 1) SS BOND : angle 3.16241 ( 2) covalent geometry : bond 0.00328 ( 7548) covalent geometry : angle 0.64774 (10279) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.9652 (t80) cc_final: 0.9418 (t80) REVERT: A 485 MET cc_start: 0.9155 (mmt) cc_final: 0.8232 (ppp) outliers start: 15 outliers final: 10 residues processed: 58 average time/residue: 0.1538 time to fit residues: 13.8219 Evaluate side-chains 51 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 444 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 70 optimal weight: 0.0020 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.046068 restraints weight = 28180.358| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.69 r_work: 0.2655 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7557 Z= 0.107 Angle : 0.646 11.062 10305 Z= 0.286 Chirality : 0.041 0.318 1216 Planarity : 0.003 0.053 1272 Dihedral : 15.096 116.957 1158 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.03 % Allowed : 16.60 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 930 helix: 2.62 (0.24), residues: 493 sheet: -0.70 (0.61), residues: 63 loop : -0.85 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 405 HIS 0.005 0.001 HIS B 367 PHE 0.021 0.001 PHE B 403 TYR 0.019 0.001 TYR A 251 ARG 0.001 0.000 ARG B 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00978 ( 4) link_NAG-ASN : angle 4.12103 ( 12) link_BETA1-4 : bond 0.00876 ( 4) link_BETA1-4 : angle 4.61190 ( 12) hydrogen bonds : bond 0.03459 ( 393) hydrogen bonds : angle 4.05822 ( 1134) SS BOND : bond 0.00513 ( 1) SS BOND : angle 2.91749 ( 2) covalent geometry : bond 0.00226 ( 7548) covalent geometry : angle 0.60969 (10279) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.9671 (t80) cc_final: 0.9413 (t80) REVERT: A 485 MET cc_start: 0.9143 (mmt) cc_final: 0.8214 (ppp) REVERT: B 296 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8321 (t80) REVERT: B 365 MET cc_start: 0.9528 (tpp) cc_final: 0.8679 (tpp) outliers start: 16 outliers final: 8 residues processed: 59 average time/residue: 0.1408 time to fit residues: 12.9160 Evaluate side-chains 53 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 296 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.043999 restraints weight = 28829.523| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 4.67 r_work: 0.2597 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7557 Z= 0.180 Angle : 0.666 11.232 10305 Z= 0.302 Chirality : 0.042 0.320 1216 Planarity : 0.004 0.050 1272 Dihedral : 14.381 117.067 1158 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.28 % Allowed : 17.49 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 930 helix: 2.60 (0.24), residues: 493 sheet: -0.77 (0.61), residues: 63 loop : -0.85 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.005 0.001 HIS B 367 PHE 0.027 0.001 PHE B 403 TYR 0.020 0.001 TYR A 251 ARG 0.003 0.000 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00885 ( 4) link_NAG-ASN : angle 4.16456 ( 12) link_BETA1-4 : bond 0.00768 ( 4) link_BETA1-4 : angle 4.59895 ( 12) hydrogen bonds : bond 0.04083 ( 393) hydrogen bonds : angle 4.19078 ( 1134) SS BOND : bond 0.00472 ( 1) SS BOND : angle 2.82785 ( 2) covalent geometry : bond 0.00412 ( 7548) covalent geometry : angle 0.63108 (10279) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 485 MET cc_start: 0.9191 (mmt) cc_final: 0.8578 (ppp) REVERT: B 365 MET cc_start: 0.9515 (tpp) cc_final: 0.9305 (tpp) outliers start: 18 outliers final: 10 residues processed: 56 average time/residue: 0.1836 time to fit residues: 15.6686 Evaluate side-chains 47 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 444 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.044967 restraints weight = 28399.317| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 4.72 r_work: 0.2621 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7557 Z= 0.121 Angle : 0.652 11.157 10305 Z= 0.292 Chirality : 0.042 0.313 1216 Planarity : 0.004 0.051 1272 Dihedral : 13.815 117.251 1158 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.41 % Allowed : 18.38 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.29), residues: 930 helix: 2.58 (0.24), residues: 493 sheet: -0.78 (0.61), residues: 63 loop : -0.86 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 405 HIS 0.004 0.001 HIS B 367 PHE 0.024 0.001 PHE B 403 TYR 0.017 0.001 TYR A 423 ARG 0.007 0.000 ARG A 614 Details of bonding type rmsd link_NAG-ASN : bond 0.00932 ( 4) link_NAG-ASN : angle 4.15796 ( 12) link_BETA1-4 : bond 0.00767 ( 4) link_BETA1-4 : angle 4.64405 ( 12) hydrogen bonds : bond 0.03734 ( 393) hydrogen bonds : angle 4.07796 ( 1134) SS BOND : bond 0.00464 ( 1) SS BOND : angle 2.74167 ( 2) covalent geometry : bond 0.00268 ( 7548) covalent geometry : angle 0.61547 (10279) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 MET cc_start: 0.9182 (mmt) cc_final: 0.8239 (ppp) REVERT: B 296 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.8473 (t80) REVERT: B 365 MET cc_start: 0.9660 (tpp) cc_final: 0.9296 (mtp) outliers start: 19 outliers final: 14 residues processed: 59 average time/residue: 0.1766 time to fit residues: 16.4563 Evaluate side-chains 55 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 466 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 89 optimal weight: 0.0020 chunk 67 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.0070 chunk 46 optimal weight: 10.0000 chunk 75 optimal weight: 0.0020 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.067869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.046637 restraints weight = 28196.362| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 4.73 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7557 Z= 0.105 Angle : 0.647 11.116 10305 Z= 0.288 Chirality : 0.041 0.309 1216 Planarity : 0.003 0.054 1272 Dihedral : 13.198 117.056 1158 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.39 % Allowed : 19.90 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.29), residues: 930 helix: 2.53 (0.24), residues: 493 sheet: -0.70 (0.61), residues: 63 loop : -0.85 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 PHE 0.024 0.001 PHE B 403 TYR 0.024 0.001 TYR A 251 ARG 0.002 0.000 ARG A 614 Details of bonding type rmsd link_NAG-ASN : bond 0.00956 ( 4) link_NAG-ASN : angle 4.17435 ( 12) link_BETA1-4 : bond 0.00791 ( 4) link_BETA1-4 : angle 4.67118 ( 12) hydrogen bonds : bond 0.03153 ( 393) hydrogen bonds : angle 3.98139 ( 1134) SS BOND : bond 0.00465 ( 1) SS BOND : angle 2.61099 ( 2) covalent geometry : bond 0.00220 ( 7548) covalent geometry : angle 0.61062 (10279) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 MET cc_start: 0.9169 (mmt) cc_final: 0.8300 (ppp) REVERT: B 296 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8501 (t80) REVERT: B 365 MET cc_start: 0.9573 (tpp) cc_final: 0.9117 (tpp) outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 0.1516 time to fit residues: 13.2631 Evaluate side-chains 51 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 487 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.067520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.046222 restraints weight = 28529.563| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.77 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7557 Z= 0.109 Angle : 0.648 11.070 10305 Z= 0.290 Chirality : 0.041 0.315 1216 Planarity : 0.003 0.053 1272 Dihedral : 12.850 116.934 1158 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.01 % Allowed : 20.53 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.29), residues: 930 helix: 2.55 (0.24), residues: 493 sheet: -0.68 (0.62), residues: 63 loop : -0.87 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.003 0.001 HIS B 367 PHE 0.024 0.001 PHE B 403 TYR 0.018 0.001 TYR A 251 ARG 0.003 0.000 ARG A 614 Details of bonding type rmsd link_NAG-ASN : bond 0.00958 ( 4) link_NAG-ASN : angle 4.15674 ( 12) link_BETA1-4 : bond 0.00787 ( 4) link_BETA1-4 : angle 4.66637 ( 12) hydrogen bonds : bond 0.03211 ( 393) hydrogen bonds : angle 3.96756 ( 1134) SS BOND : bond 0.00425 ( 1) SS BOND : angle 2.53655 ( 2) covalent geometry : bond 0.00240 ( 7548) covalent geometry : angle 0.61186 (10279) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 MET cc_start: 0.9192 (mmt) cc_final: 0.8318 (ppp) REVERT: B 296 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8526 (t80) REVERT: B 365 MET cc_start: 0.9568 (tpp) cc_final: 0.9078 (tpp) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.1573 time to fit residues: 12.6655 Evaluate side-chains 52 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 487 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 0.0030 chunk 70 optimal weight: 0.9980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.067964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.046639 restraints weight = 28718.742| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 4.83 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7557 Z= 0.105 Angle : 0.643 11.092 10305 Z= 0.288 Chirality : 0.041 0.313 1216 Planarity : 0.003 0.053 1272 Dihedral : 12.296 117.135 1158 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.14 % Allowed : 20.53 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.29), residues: 930 helix: 2.56 (0.24), residues: 493 sheet: -0.64 (0.62), residues: 63 loop : -0.86 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 405 HIS 0.002 0.001 HIS B 367 PHE 0.026 0.001 PHE B 403 TYR 0.025 0.001 TYR A 251 ARG 0.003 0.000 ARG A 614 Details of bonding type rmsd link_NAG-ASN : bond 0.00979 ( 4) link_NAG-ASN : angle 4.19875 ( 12) link_BETA1-4 : bond 0.00879 ( 4) link_BETA1-4 : angle 4.69538 ( 12) hydrogen bonds : bond 0.03035 ( 393) hydrogen bonds : angle 3.92855 ( 1134) SS BOND : bond 0.00442 ( 1) SS BOND : angle 2.50879 ( 2) covalent geometry : bond 0.00226 ( 7548) covalent geometry : angle 0.60583 (10279) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 MET cc_start: 0.9191 (mmt) cc_final: 0.8319 (ppp) REVERT: B 296 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.8585 (t80) REVERT: B 365 MET cc_start: 0.9561 (tpp) cc_final: 0.9054 (tpp) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.1643 time to fit residues: 14.0093 Evaluate side-chains 55 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 487 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.046252 restraints weight = 28381.050| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 4.70 r_work: 0.2652 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7557 Z= 0.119 Angle : 0.647 11.081 10305 Z= 0.291 Chirality : 0.041 0.313 1216 Planarity : 0.003 0.052 1272 Dihedral : 12.041 117.333 1158 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.52 % Allowed : 20.41 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 930 helix: 2.58 (0.24), residues: 493 sheet: -0.65 (0.62), residues: 63 loop : -0.86 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.003 0.001 HIS B 367 PHE 0.025 0.001 PHE B 403 TYR 0.006 0.001 TYR B 387 ARG 0.002 0.000 ARG B 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00952 ( 4) link_NAG-ASN : angle 4.17885 ( 12) link_BETA1-4 : bond 0.00889 ( 4) link_BETA1-4 : angle 4.67263 ( 12) hydrogen bonds : bond 0.03244 ( 393) hydrogen bonds : angle 3.95547 ( 1134) SS BOND : bond 0.00408 ( 1) SS BOND : angle 2.45887 ( 2) covalent geometry : bond 0.00266 ( 7548) covalent geometry : angle 0.61047 (10279) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3482.18 seconds wall clock time: 61 minutes 18.51 seconds (3678.51 seconds total)