Starting phenix.real_space_refine on Tue Mar 3 16:24:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uzl_20962/03_2026/6uzl_20962.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uzl_20962/03_2026/6uzl_20962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uzl_20962/03_2026/6uzl_20962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uzl_20962/03_2026/6uzl_20962.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uzl_20962/03_2026/6uzl_20962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uzl_20962/03_2026/6uzl_20962.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 44 5.16 5 C 4412 2.51 5 N 1250 2.21 5 O 1302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7008 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3502 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PTRANS': 13, 'TRANS': 517} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 621 Unresolved non-hydrogen angles: 794 Unresolved non-hydrogen dihedrals: 486 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLU:plan': 16, 'ARG:plan': 19, 'ASP:plan': 14, 'PHE:plan': 5, 'ASN:plan1': 12, 'TYR:plan': 6, 'HIS:plan': 3, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 356 Chain: "B" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3506 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PTRANS': 13, 'TRANS': 517} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 789 Unresolved non-hydrogen dihedrals: 483 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 19, 'ASP:plan': 14, 'PHE:plan': 5, 'ASN:plan1': 12, 'TYR:plan': 6, 'HIS:plan': 3, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 352 Time building chain proxies: 1.51, per 1000 atoms: 0.22 Number of scatterers: 7008 At special positions: 0 Unit cell: (73, 86, 124, 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 44 16.00 O 1302 8.00 N 1250 7.00 C 4412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 218.4 milliseconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 2 sheets defined 72.8% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.734A pdb=" N LEU A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 23 through 54 removed outlier: 3.700A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 48 " --> pdb=" O MET A 44 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 111 removed outlier: 4.281A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.701A pdb=" N LYS A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 162 removed outlier: 4.645A pdb=" N ILE A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 193 Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 195 through 221 removed outlier: 3.650A pdb=" N THR A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 268 removed outlier: 3.891A pdb=" N SER A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 280 through 324 Proline residue: A 297 - end of helix removed outlier: 4.477A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.604A pdb=" N SER A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 446 through 458 Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.618A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 474 through 479 removed outlier: 4.015A pdb=" N VAL A 479 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 512 through 528 Processing helix chain 'B' and resid 12 through 21 Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 23 through 54 removed outlier: 3.864A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 61 through 110 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.858A pdb=" N GLN B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 162 Processing helix chain 'B' and resid 164 through 213 Proline residue: B 176 - end of helix removed outlier: 3.897A pdb=" N GLY B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 222 through 272 removed outlier: 3.760A pdb=" N GLU B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 280 through 324 Proline residue: B 297 - end of helix removed outlier: 3.875A pdb=" N ASN B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLN B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 401 through 405 removed outlier: 3.701A pdb=" N GLY B 404 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 419 removed outlier: 3.653A pdb=" N ARG B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 465 removed outlier: 3.686A pdb=" N ILE B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 464 " --> pdb=" O MET B 460 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 459 through 465' Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.924A pdb=" N VAL B 479 " --> pdb=" O GLU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 512 through 528 Processing sheet with id=AA1, first strand: chain 'A' and resid 362 through 366 removed outlier: 4.932A pdb=" N ILE A 362 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 346 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 568 hydrogen bonds defined for protein. 1677 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: 1.04 Time building geometry restraints manager: 0.82 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: 2375 1.34 - 1.46: 1326 1.46 - 1.58: 3305 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 7090 Sorted by residual: bond pdb=" CA LEU A 374 " pdb=" C LEU A 374 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.34e-02 5.57e+03 3.64e+01 bond pdb=" CA ARG B 360 " pdb=" C ARG B 360 " ideal model delta sigma weight residual 1.523 1.565 -0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" N LEU B 359 " pdb=" CA LEU B 359 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.13e+00 bond pdb=" CA ALA B 358 " pdb=" C ALA B 358 " ideal model delta sigma weight residual 1.521 1.556 -0.035 1.20e-02 6.94e+03 8.45e+00 bond pdb=" CA PRO B 357 " pdb=" C PRO B 357 " ideal model delta sigma weight residual 1.520 1.558 -0.039 1.42e-02 4.96e+03 7.44e+00 ... (remaining 7085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 9477 2.87 - 5.73: 148 5.73 - 8.60: 31 8.60 - 11.46: 3 11.46 - 14.33: 2 Bond angle restraints: 9661 Sorted by residual: angle pdb=" N ARG B 360 " pdb=" CA ARG B 360 " pdb=" C ARG B 360 " ideal model delta sigma weight residual 111.28 125.61 -14.33 1.09e+00 8.42e-01 1.73e+02 angle pdb=" N THR B 348 " pdb=" CA THR B 348 " pdb=" C THR B 348 " ideal model delta sigma weight residual 110.35 121.78 -11.43 1.36e+00 5.41e-01 7.06e+01 angle pdb=" C ILE B 366 " pdb=" N PRO B 367 " pdb=" CA PRO B 367 " ideal model delta sigma weight residual 119.76 127.63 -7.87 1.03e+00 9.43e-01 5.84e+01 angle pdb=" N LEU B 364 " pdb=" CA LEU B 364 " pdb=" C LEU B 364 " ideal model delta sigma weight residual 109.60 119.00 -9.40 1.53e+00 4.27e-01 3.78e+01 angle pdb=" N PRO B 352 " pdb=" CA PRO B 352 " pdb=" C PRO B 352 " ideal model delta sigma weight residual 112.47 100.15 12.32 2.06e+00 2.36e-01 3.58e+01 ... (remaining 9656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.92: 3805 14.92 - 29.84: 338 29.84 - 44.77: 87 44.77 - 59.69: 13 59.69 - 74.61: 6 Dihedral angle restraints: 4249 sinusoidal: 1189 harmonic: 3060 Sorted by residual: dihedral pdb=" CA TYR B 410 " pdb=" C TYR B 410 " pdb=" N THR B 411 " pdb=" CA THR B 411 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA TYR A 351 " pdb=" C TYR A 351 " pdb=" N PRO A 352 " pdb=" CA PRO A 352 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ARG A 408 " pdb=" C ARG A 408 " pdb=" N GLU A 409 " pdb=" CA GLU A 409 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 4246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1096 0.086 - 0.171: 104 0.171 - 0.256: 8 0.256 - 0.342: 3 0.342 - 0.427: 1 Chirality restraints: 1212 Sorted by residual: chirality pdb=" CA ARG B 360 " pdb=" N ARG B 360 " pdb=" C ARG B 360 " pdb=" CB ARG B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA THR B 348 " pdb=" N THR B 348 " pdb=" C THR B 348 " pdb=" CB THR B 348 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ILE B 395 " pdb=" N ILE B 395 " pdb=" C ILE B 395 " pdb=" CB ILE B 395 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1209 not shown) Planarity restraints: 1249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 356 " 0.018 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C VAL B 356 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL B 356 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO B 357 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 272 " -0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO B 273 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 273 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 273 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 329 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C ASP B 329 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP B 329 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU B 330 " 0.013 2.00e-02 2.50e+03 ... (remaining 1246 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 900 2.74 - 3.28: 8956 3.28 - 3.82: 11836 3.82 - 4.36: 13870 4.36 - 4.90: 20724 Nonbonded interactions: 56286 Sorted by model distance: nonbonded pdb=" O ASN A 37 " pdb=" OG SER A 40 " model vdw 2.198 3.040 nonbonded pdb=" O GLY A 282 " pdb=" OG1 THR A 285 " model vdw 2.201 3.040 nonbonded pdb=" O ILE B 128 " pdb=" OG SER B 132 " model vdw 2.202 3.040 nonbonded pdb=" O ALA B 368 " pdb=" N LYS B 370 " model vdw 2.204 3.120 nonbonded pdb=" O ALA B 314 " pdb=" OG1 THR B 317 " model vdw 2.204 3.040 ... (remaining 56281 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 'A' selection = (chain 'B' and (resid 11 through 148 or (resid 149 and (name N or name CA or nam \ e C or name O or name CB )) or resid 150 through 541)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.005 0.081 7090 Z= 0.319 Angle : 1.004 14.330 9661 Z= 0.657 Chirality : 0.053 0.427 1212 Planarity : 0.005 0.083 1249 Dihedral : 13.211 74.610 2261 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.12 % Favored : 84.12 % Rotamer: Outliers : 0.18 % Allowed : 8.17 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.19), residues: 1058 helix: -2.76 (0.14), residues: 692 sheet: -2.46 (0.91), residues: 29 loop : -3.69 (0.27), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 229 TYR 0.011 0.002 TYR A 83 PHE 0.021 0.002 PHE B 157 TRP 0.024 0.002 TRP B 91 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 7090) covalent geometry : angle 1.00423 ( 9661) hydrogen bonds : bond 0.16964 ( 568) hydrogen bonds : angle 7.28130 ( 1677) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.9183 (mmm) cc_final: 0.8790 (mmm) REVERT: A 83 TYR cc_start: 0.8478 (m-10) cc_final: 0.8029 (m-80) REVERT: A 98 MET cc_start: 0.8924 (mmm) cc_final: 0.8520 (tpp) REVERT: A 105 PHE cc_start: 0.9279 (m-10) cc_final: 0.8804 (m-80) REVERT: A 111 MET cc_start: 0.9219 (mmp) cc_final: 0.8914 (mmm) REVERT: A 133 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8944 (pt0) REVERT: A 156 LEU cc_start: 0.9561 (mt) cc_final: 0.9226 (pp) REVERT: A 158 ILE cc_start: 0.9469 (mm) cc_final: 0.9222 (mm) REVERT: A 161 PHE cc_start: 0.8924 (m-10) cc_final: 0.8596 (m-10) REVERT: A 209 GLN cc_start: 0.9219 (pt0) cc_final: 0.8728 (tm-30) REVERT: A 228 LYS cc_start: 0.9699 (mttt) cc_final: 0.9318 (mmtm) REVERT: A 231 ASP cc_start: 0.9302 (m-30) cc_final: 0.9089 (m-30) REVERT: A 267 LEU cc_start: 0.9493 (mt) cc_final: 0.9285 (mt) REVERT: A 291 MET cc_start: 0.9079 (mmm) cc_final: 0.8647 (tpt) REVERT: A 296 ARG cc_start: 0.5657 (mtt180) cc_final: 0.4849 (ttm170) REVERT: A 303 ASN cc_start: 0.9512 (m-40) cc_final: 0.9244 (p0) REVERT: A 312 MET cc_start: 0.8752 (mmm) cc_final: 0.8348 (mtt) REVERT: B 74 LEU cc_start: 0.9685 (mt) cc_final: 0.9440 (mt) REVERT: B 75 MET cc_start: 0.9407 (mmm) cc_final: 0.8854 (mmm) REVERT: B 83 TYR cc_start: 0.8427 (m-10) cc_final: 0.8077 (m-80) REVERT: B 98 MET cc_start: 0.9250 (ttm) cc_final: 0.8961 (ttm) REVERT: B 105 PHE cc_start: 0.9308 (m-80) cc_final: 0.8949 (m-80) REVERT: B 131 ASP cc_start: 0.8734 (m-30) cc_final: 0.8424 (m-30) REVERT: B 159 MET cc_start: 0.8620 (mmp) cc_final: 0.7701 (tpp) REVERT: B 161 PHE cc_start: 0.8780 (m-10) cc_final: 0.8437 (m-10) REVERT: B 163 TYR cc_start: 0.8903 (m-10) cc_final: 0.7259 (m-80) REVERT: B 215 LYS cc_start: 0.9564 (mttt) cc_final: 0.9363 (mmtt) REVERT: B 228 LYS cc_start: 0.9834 (mttt) cc_final: 0.9404 (mmmm) REVERT: B 261 LEU cc_start: 0.9463 (mt) cc_final: 0.8968 (tp) REVERT: B 296 ARG cc_start: 0.5254 (mtt180) cc_final: 0.4609 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.0740 time to fit residues: 22.7009 Evaluate side-chains 187 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 50.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 191 ASN A 303 ASN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.081738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.063085 restraints weight = 29447.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.065045 restraints weight = 18998.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066556 restraints weight = 13642.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.067696 restraints weight = 10466.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.068516 restraints weight = 8449.280| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7090 Z= 0.178 Angle : 0.677 6.759 9661 Z= 0.369 Chirality : 0.045 0.145 1212 Planarity : 0.005 0.092 1249 Dihedral : 4.808 21.921 1106 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.54 % Allowed : 5.44 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.24), residues: 1058 helix: -0.46 (0.18), residues: 725 sheet: -1.83 (0.88), residues: 34 loop : -2.85 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 78 TYR 0.006 0.001 TYR A 87 PHE 0.030 0.002 PHE A 308 TRP 0.021 0.002 TRP A 66 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7090) covalent geometry : angle 0.67652 ( 9661) hydrogen bonds : bond 0.05420 ( 568) hydrogen bonds : angle 5.35511 ( 1677) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 251 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8843 (m-30) cc_final: 0.8360 (m-30) REVERT: A 105 PHE cc_start: 0.9485 (m-10) cc_final: 0.9162 (m-80) REVERT: A 107 HIS cc_start: 0.8593 (m-70) cc_final: 0.8219 (m170) REVERT: A 111 MET cc_start: 0.9515 (mmp) cc_final: 0.9083 (mmp) REVERT: A 133 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9020 (pt0) REVERT: A 158 ILE cc_start: 0.9396 (mm) cc_final: 0.9137 (mm) REVERT: A 161 PHE cc_start: 0.8906 (m-10) cc_final: 0.8461 (m-10) REVERT: A 208 GLU cc_start: 0.9406 (tm-30) cc_final: 0.9168 (tm-30) REVERT: A 209 GLN cc_start: 0.9066 (pt0) cc_final: 0.8698 (tm-30) REVERT: A 211 LEU cc_start: 0.9653 (mt) cc_final: 0.9114 (mp) REVERT: A 224 GLU cc_start: 0.9433 (mp0) cc_final: 0.9029 (mp0) REVERT: A 228 LYS cc_start: 0.9631 (mttt) cc_final: 0.9304 (mmtm) REVERT: A 231 ASP cc_start: 0.9346 (m-30) cc_final: 0.8884 (m-30) REVERT: A 235 ASN cc_start: 0.9497 (m-40) cc_final: 0.8760 (m-40) REVERT: A 237 MET cc_start: 0.9397 (mmp) cc_final: 0.9169 (mmm) REVERT: A 242 MET cc_start: 0.9121 (mmm) cc_final: 0.8911 (mmm) REVERT: A 261 LEU cc_start: 0.8954 (mp) cc_final: 0.8636 (tp) REVERT: A 288 PHE cc_start: 0.9614 (m-10) cc_final: 0.9413 (m-10) REVERT: A 291 MET cc_start: 0.9203 (mmm) cc_final: 0.8811 (tpt) REVERT: A 296 ARG cc_start: 0.5862 (mtt180) cc_final: 0.5634 (ttt180) REVERT: A 312 MET cc_start: 0.9014 (mmm) cc_final: 0.8511 (mpp) REVERT: B 54 ASP cc_start: 0.9345 (m-30) cc_final: 0.8932 (t0) REVERT: B 67 MET cc_start: 0.9352 (mpp) cc_final: 0.8973 (mpp) REVERT: B 75 MET cc_start: 0.9578 (mmm) cc_final: 0.8943 (mmm) REVERT: B 87 TYR cc_start: 0.8689 (t80) cc_final: 0.8482 (t80) REVERT: B 98 MET cc_start: 0.9423 (ttm) cc_final: 0.8838 (ttm) REVERT: B 105 PHE cc_start: 0.9368 (m-80) cc_final: 0.9105 (m-80) REVERT: B 121 THR cc_start: 0.9482 (p) cc_final: 0.9269 (t) REVERT: B 131 ASP cc_start: 0.8671 (m-30) cc_final: 0.8362 (m-30) REVERT: B 161 PHE cc_start: 0.8715 (m-10) cc_final: 0.8310 (m-10) REVERT: B 196 MET cc_start: 0.7910 (tpt) cc_final: 0.7650 (tpp) REVERT: B 200 MET cc_start: 0.8928 (mtm) cc_final: 0.8609 (mmm) REVERT: B 215 LYS cc_start: 0.9550 (mttt) cc_final: 0.9267 (mmtt) REVERT: B 228 LYS cc_start: 0.9816 (mttt) cc_final: 0.9408 (mmmm) REVERT: B 242 MET cc_start: 0.9196 (mmt) cc_final: 0.8904 (mmm) REVERT: B 261 LEU cc_start: 0.9285 (mt) cc_final: 0.8965 (tp) REVERT: B 284 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9313 (mp) REVERT: B 288 PHE cc_start: 0.9537 (m-10) cc_final: 0.9295 (m-10) REVERT: B 291 MET cc_start: 0.9361 (ttt) cc_final: 0.8541 (tpt) REVERT: B 296 ARG cc_start: 0.5010 (mtt180) cc_final: 0.4349 (ttm170) REVERT: B 328 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8451 (mmtt) REVERT: B 329 ASP cc_start: 0.8754 (m-30) cc_final: 0.7958 (t0) outliers start: 3 outliers final: 0 residues processed: 251 average time/residue: 0.0603 time to fit residues: 21.4699 Evaluate side-chains 199 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 0.0370 chunk 44 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 240 GLN B 256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.080615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.062138 restraints weight = 29171.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.064140 restraints weight = 19286.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065636 restraints weight = 13953.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.066790 restraints weight = 10775.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067664 restraints weight = 8758.774| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7090 Z= 0.166 Angle : 0.628 6.865 9661 Z= 0.339 Chirality : 0.044 0.171 1212 Planarity : 0.005 0.091 1249 Dihedral : 4.432 22.212 1106 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.18 % Allowed : 3.27 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.26), residues: 1058 helix: 0.59 (0.19), residues: 729 sheet: -1.87 (0.79), residues: 39 loop : -2.60 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 238 TYR 0.014 0.001 TYR A 163 PHE 0.014 0.002 PHE B 308 TRP 0.013 0.002 TRP B 66 HIS 0.003 0.002 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7090) covalent geometry : angle 0.62754 ( 9661) hydrogen bonds : bond 0.04950 ( 568) hydrogen bonds : angle 4.99964 ( 1677) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.9104 (t0) cc_final: 0.8727 (t0) REVERT: A 47 LEU cc_start: 0.9581 (mt) cc_final: 0.9357 (mt) REVERT: A 53 ASP cc_start: 0.8724 (m-30) cc_final: 0.8507 (m-30) REVERT: A 75 MET cc_start: 0.9461 (mmm) cc_final: 0.9020 (mmm) REVERT: A 105 PHE cc_start: 0.9528 (m-80) cc_final: 0.9041 (m-80) REVERT: A 107 HIS cc_start: 0.8628 (m-70) cc_final: 0.8201 (m170) REVERT: A 133 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8983 (pt0) REVERT: A 158 ILE cc_start: 0.9305 (mm) cc_final: 0.9047 (mm) REVERT: A 161 PHE cc_start: 0.8804 (m-10) cc_final: 0.8350 (m-10) REVERT: A 209 GLN cc_start: 0.9113 (pt0) cc_final: 0.8886 (tm-30) REVERT: A 211 LEU cc_start: 0.9629 (mt) cc_final: 0.9333 (mt) REVERT: A 214 HIS cc_start: 0.8232 (m90) cc_final: 0.7148 (m-70) REVERT: A 231 ASP cc_start: 0.9295 (m-30) cc_final: 0.8794 (m-30) REVERT: A 235 ASN cc_start: 0.9460 (m-40) cc_final: 0.8711 (m-40) REVERT: A 288 PHE cc_start: 0.9595 (m-10) cc_final: 0.9390 (m-10) REVERT: A 291 MET cc_start: 0.9189 (mmm) cc_final: 0.8734 (tpt) REVERT: A 296 ARG cc_start: 0.5812 (mtt180) cc_final: 0.5062 (mtt180) REVERT: A 303 ASN cc_start: 0.9529 (m110) cc_final: 0.9128 (p0) REVERT: A 312 MET cc_start: 0.9015 (mmm) cc_final: 0.8306 (mtt) REVERT: B 54 ASP cc_start: 0.9303 (m-30) cc_final: 0.8920 (t0) REVERT: B 75 MET cc_start: 0.9576 (mmm) cc_final: 0.8933 (mmm) REVERT: B 87 TYR cc_start: 0.8732 (t80) cc_final: 0.8498 (t80) REVERT: B 98 MET cc_start: 0.9389 (ttm) cc_final: 0.8960 (ttm) REVERT: B 105 PHE cc_start: 0.9412 (m-80) cc_final: 0.9145 (m-80) REVERT: B 121 THR cc_start: 0.9473 (p) cc_final: 0.9251 (t) REVERT: B 131 ASP cc_start: 0.8696 (m-30) cc_final: 0.8474 (m-30) REVERT: B 161 PHE cc_start: 0.8780 (m-10) cc_final: 0.8324 (m-10) REVERT: B 200 MET cc_start: 0.8978 (mtm) cc_final: 0.8663 (mmm) REVERT: B 211 LEU cc_start: 0.9847 (mt) cc_final: 0.9609 (mt) REVERT: B 215 LYS cc_start: 0.9476 (mttt) cc_final: 0.9245 (mmmt) REVERT: B 228 LYS cc_start: 0.9809 (mttt) cc_final: 0.9473 (mmmm) REVERT: B 242 MET cc_start: 0.9235 (mmt) cc_final: 0.8950 (mmm) REVERT: B 244 MET cc_start: 0.9466 (ttp) cc_final: 0.9202 (ttp) REVERT: B 261 LEU cc_start: 0.9164 (mt) cc_final: 0.8829 (tp) REVERT: B 284 ILE cc_start: 0.9592 (mp) cc_final: 0.9370 (mp) REVERT: B 288 PHE cc_start: 0.9531 (m-10) cc_final: 0.9312 (m-10) REVERT: B 291 MET cc_start: 0.9313 (ttt) cc_final: 0.8494 (tpt) REVERT: B 296 ARG cc_start: 0.5220 (mtt180) cc_final: 0.4614 (ttp-170) REVERT: B 328 LYS cc_start: 0.9005 (mmtm) cc_final: 0.8499 (mmtt) REVERT: B 329 ASP cc_start: 0.8724 (m-30) cc_final: 0.7941 (t0) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.0551 time to fit residues: 19.5883 Evaluate side-chains 199 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 30.0000 chunk 104 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 102 optimal weight: 30.0000 chunk 85 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** A 214 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 = 0.3509 r_free = 0.3509 target = 0.081474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.062814 restraints weight = 29273.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064824 restraints weight = 19344.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.066384 restraints weight = 14074.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067583 restraints weight = 10852.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068513 restraints weight = 8783.453| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7090 Z= 0.156 Angle : 0.619 8.296 9661 Z= 0.330 Chirality : 0.043 0.175 1212 Planarity : 0.005 0.091 1249 Dihedral : 4.207 19.302 1106 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.18 % Allowed : 2.54 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.26), residues: 1058 helix: 1.02 (0.19), residues: 731 sheet: -1.31 (1.04), residues: 24 loop : -2.43 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 238 TYR 0.005 0.001 TYR A 163 PHE 0.024 0.002 PHE B 43 TRP 0.012 0.001 TRP B 66 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7090) covalent geometry : angle 0.61944 ( 9661) hydrogen bonds : bond 0.04702 ( 568) hydrogen bonds : angle 4.79167 ( 1677) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.9161 (t0) cc_final: 0.8838 (t0) REVERT: A 41 ASP cc_start: 0.8628 (m-30) cc_final: 0.8404 (m-30) REVERT: A 47 LEU cc_start: 0.9572 (mt) cc_final: 0.9318 (mt) REVERT: A 75 MET cc_start: 0.9423 (mmm) cc_final: 0.9133 (mmm) REVERT: A 105 PHE cc_start: 0.9465 (m-80) cc_final: 0.8970 (m-80) REVERT: A 107 HIS cc_start: 0.8599 (m-70) cc_final: 0.8193 (m170) REVERT: A 121 THR cc_start: 0.9426 (p) cc_final: 0.9139 (p) REVERT: A 125 LEU cc_start: 0.9510 (mt) cc_final: 0.9253 (mt) REVERT: A 131 ASP cc_start: 0.8617 (m-30) cc_final: 0.8412 (m-30) REVERT: A 133 GLU cc_start: 0.9393 (mt-10) cc_final: 0.8941 (pt0) REVERT: A 160 MET cc_start: 0.9209 (ptp) cc_final: 0.8997 (ptp) REVERT: A 161 PHE cc_start: 0.8778 (m-10) cc_final: 0.8301 (m-10) REVERT: A 211 LEU cc_start: 0.9731 (mt) cc_final: 0.9447 (mt) REVERT: A 291 MET cc_start: 0.9157 (mmm) cc_final: 0.8712 (tpt) REVERT: A 296 ARG cc_start: 0.5685 (mtt180) cc_final: 0.5005 (ttm170) REVERT: A 303 ASN cc_start: 0.9509 (m110) cc_final: 0.9137 (p0) REVERT: A 312 MET cc_start: 0.8988 (mmm) cc_final: 0.8328 (mtt) REVERT: B 54 ASP cc_start: 0.9343 (m-30) cc_final: 0.8866 (t0) REVERT: B 67 MET cc_start: 0.9314 (mpp) cc_final: 0.9089 (mpp) REVERT: B 75 MET cc_start: 0.9535 (mmm) cc_final: 0.9302 (mmm) REVERT: B 87 TYR cc_start: 0.8813 (t80) cc_final: 0.8540 (t80) REVERT: B 98 MET cc_start: 0.9353 (ttm) cc_final: 0.7909 (ttm) REVERT: B 102 ARG cc_start: 0.9208 (ttm170) cc_final: 0.8289 (ttm170) REVERT: B 105 PHE cc_start: 0.9405 (m-10) cc_final: 0.8994 (m-80) REVERT: B 108 MET cc_start: 0.9121 (mtm) cc_final: 0.8619 (ptt) REVERT: B 121 THR cc_start: 0.9473 (p) cc_final: 0.9199 (t) REVERT: B 131 ASP cc_start: 0.8611 (m-30) cc_final: 0.8368 (m-30) REVERT: B 161 PHE cc_start: 0.8736 (m-10) cc_final: 0.8330 (m-10) REVERT: B 163 TYR cc_start: 0.8444 (m-10) cc_final: 0.7651 (m-80) REVERT: B 200 MET cc_start: 0.8753 (mtm) cc_final: 0.8529 (mmm) REVERT: B 210 MET cc_start: 0.8279 (mmp) cc_final: 0.8071 (mmp) REVERT: B 211 LEU cc_start: 0.9822 (mt) cc_final: 0.9194 (pp) REVERT: B 215 LYS cc_start: 0.9462 (mttt) cc_final: 0.9222 (mmmt) REVERT: B 231 ASP cc_start: 0.9513 (m-30) cc_final: 0.9066 (m-30) REVERT: B 235 ASN cc_start: 0.9570 (m-40) cc_final: 0.9315 (m-40) REVERT: B 242 MET cc_start: 0.9180 (mmt) cc_final: 0.8895 (mmm) REVERT: B 261 LEU cc_start: 0.9156 (mt) cc_final: 0.8868 (tp) REVERT: B 284 ILE cc_start: 0.9583 (mp) cc_final: 0.9352 (mp) REVERT: B 288 PHE cc_start: 0.9496 (m-10) cc_final: 0.9287 (m-10) REVERT: B 291 MET cc_start: 0.9298 (ttt) cc_final: 0.8482 (tpt) REVERT: B 296 ARG cc_start: 0.5361 (mtt180) cc_final: 0.4715 (ttm170) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.0579 time to fit residues: 20.2278 Evaluate side-chains 197 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 99 optimal weight: 50.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.084356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064399 restraints weight = 29280.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.066443 restraints weight = 19690.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067997 restraints weight = 14390.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069172 restraints weight = 11172.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.070088 restraints weight = 9120.112| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7090 Z= 0.142 Angle : 0.604 6.701 9661 Z= 0.321 Chirality : 0.043 0.152 1212 Planarity : 0.004 0.087 1249 Dihedral : 4.062 21.439 1106 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 1058 helix: 1.33 (0.19), residues: 735 sheet: -1.23 (1.08), residues: 24 loop : -2.17 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 238 TYR 0.006 0.001 TYR B 83 PHE 0.010 0.001 PHE B 157 TRP 0.011 0.001 TRP A 66 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7090) covalent geometry : angle 0.60443 ( 9661) hydrogen bonds : bond 0.04508 ( 568) hydrogen bonds : angle 4.65865 ( 1677) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.9177 (t0) cc_final: 0.8863 (t0) REVERT: A 41 ASP cc_start: 0.8471 (m-30) cc_final: 0.8203 (m-30) REVERT: A 47 LEU cc_start: 0.9524 (mt) cc_final: 0.9243 (mt) REVERT: A 75 MET cc_start: 0.9423 (mmm) cc_final: 0.9045 (mmm) REVERT: A 105 PHE cc_start: 0.9429 (m-10) cc_final: 0.8904 (m-80) REVERT: A 107 HIS cc_start: 0.8632 (m-70) cc_final: 0.8247 (m170) REVERT: A 131 ASP cc_start: 0.8572 (m-30) cc_final: 0.8363 (m-30) REVERT: A 133 GLU cc_start: 0.9394 (mt-10) cc_final: 0.8925 (pt0) REVERT: A 159 MET cc_start: 0.8869 (tpp) cc_final: 0.8632 (tpp) REVERT: A 161 PHE cc_start: 0.8573 (m-10) cc_final: 0.8095 (m-10) REVERT: A 231 ASP cc_start: 0.9246 (m-30) cc_final: 0.8972 (m-30) REVERT: A 291 MET cc_start: 0.9106 (mmm) cc_final: 0.8682 (tpt) REVERT: A 296 ARG cc_start: 0.5707 (mtt180) cc_final: 0.5052 (ttm170) REVERT: A 303 ASN cc_start: 0.9453 (m110) cc_final: 0.9141 (p0) REVERT: A 312 MET cc_start: 0.8945 (mmm) cc_final: 0.8313 (mtt) REVERT: B 54 ASP cc_start: 0.9302 (m-30) cc_final: 0.8810 (t0) REVERT: B 67 MET cc_start: 0.9294 (mpp) cc_final: 0.9062 (mpp) REVERT: B 75 MET cc_start: 0.9480 (mmm) cc_final: 0.8715 (mmm) REVERT: B 98 MET cc_start: 0.9326 (ttm) cc_final: 0.9109 (ttm) REVERT: B 105 PHE cc_start: 0.9396 (m-10) cc_final: 0.9165 (m-80) REVERT: B 121 THR cc_start: 0.9419 (p) cc_final: 0.9141 (t) REVERT: B 131 ASP cc_start: 0.8538 (m-30) cc_final: 0.8307 (m-30) REVERT: B 156 LEU cc_start: 0.9473 (mt) cc_final: 0.9114 (pp) REVERT: B 161 PHE cc_start: 0.8520 (m-10) cc_final: 0.8099 (m-10) REVERT: B 200 MET cc_start: 0.8833 (mtm) cc_final: 0.8630 (mmm) REVERT: B 215 LYS cc_start: 0.9407 (mttt) cc_final: 0.9157 (mmmt) REVERT: B 231 ASP cc_start: 0.9375 (m-30) cc_final: 0.9000 (m-30) REVERT: B 235 ASN cc_start: 0.9493 (m-40) cc_final: 0.9189 (m-40) REVERT: B 242 MET cc_start: 0.9155 (mmt) cc_final: 0.8868 (mmm) REVERT: B 244 MET cc_start: 0.9523 (ttp) cc_final: 0.9252 (ttp) REVERT: B 261 LEU cc_start: 0.9141 (mt) cc_final: 0.8833 (tp) REVERT: B 284 ILE cc_start: 0.9545 (mp) cc_final: 0.9326 (mp) REVERT: B 291 MET cc_start: 0.9303 (ttt) cc_final: 0.8440 (tpt) REVERT: B 294 LEU cc_start: 0.9553 (mt) cc_final: 0.9301 (mt) REVERT: B 296 ARG cc_start: 0.5474 (mtt180) cc_final: 0.4912 (ttm170) REVERT: B 312 MET cc_start: 0.9044 (mmm) cc_final: 0.8162 (mmm) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.0615 time to fit residues: 22.0417 Evaluate side-chains 197 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 97 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.083346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063478 restraints weight = 30050.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.065555 restraints weight = 20210.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.067140 restraints weight = 14785.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.068305 restraints weight = 11467.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069243 restraints weight = 9342.996| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7090 Z= 0.154 Angle : 0.630 12.638 9661 Z= 0.332 Chirality : 0.044 0.170 1212 Planarity : 0.004 0.081 1249 Dihedral : 3.997 21.656 1106 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.27), residues: 1058 helix: 1.47 (0.19), residues: 724 sheet: -1.58 (1.47), residues: 14 loop : -2.02 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 148 TYR 0.007 0.001 TYR A 163 PHE 0.018 0.002 PHE A 288 TRP 0.013 0.001 TRP A 66 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7090) covalent geometry : angle 0.62971 ( 9661) hydrogen bonds : bond 0.04513 ( 568) hydrogen bonds : angle 4.69106 ( 1677) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.9135 (t0) cc_final: 0.8917 (t0) REVERT: A 41 ASP cc_start: 0.8532 (m-30) cc_final: 0.8316 (m-30) REVERT: A 47 LEU cc_start: 0.9541 (mt) cc_final: 0.9244 (mt) REVERT: A 75 MET cc_start: 0.9460 (mmm) cc_final: 0.9077 (mmm) REVERT: A 105 PHE cc_start: 0.9455 (m-10) cc_final: 0.8975 (m-80) REVERT: A 107 HIS cc_start: 0.8524 (m-70) cc_final: 0.8190 (m170) REVERT: A 131 ASP cc_start: 0.8628 (m-30) cc_final: 0.8308 (m-30) REVERT: A 133 GLU cc_start: 0.9385 (mt-10) cc_final: 0.8941 (pt0) REVERT: A 159 MET cc_start: 0.8792 (tpp) cc_final: 0.8545 (tpp) REVERT: A 161 PHE cc_start: 0.8645 (m-10) cc_final: 0.8232 (m-10) REVERT: A 211 LEU cc_start: 0.9753 (mt) cc_final: 0.9509 (mt) REVERT: A 231 ASP cc_start: 0.9246 (m-30) cc_final: 0.8880 (m-30) REVERT: A 235 ASN cc_start: 0.9436 (m-40) cc_final: 0.8896 (m110) REVERT: A 252 ASP cc_start: 0.8554 (t0) cc_final: 0.8338 (t0) REVERT: A 291 MET cc_start: 0.9154 (mmm) cc_final: 0.8782 (tpt) REVERT: A 296 ARG cc_start: 0.5774 (mtt180) cc_final: 0.5003 (mtt180) REVERT: A 303 ASN cc_start: 0.9442 (m110) cc_final: 0.9162 (p0) REVERT: A 312 MET cc_start: 0.8998 (mmm) cc_final: 0.8320 (mtt) REVERT: A 318 LEU cc_start: 0.9511 (mm) cc_final: 0.9260 (mm) REVERT: B 54 ASP cc_start: 0.9355 (m-30) cc_final: 0.8811 (t0) REVERT: B 75 MET cc_start: 0.9524 (mmm) cc_final: 0.9108 (mmm) REVERT: B 98 MET cc_start: 0.9376 (ttm) cc_final: 0.9090 (ttm) REVERT: B 105 PHE cc_start: 0.9404 (m-10) cc_final: 0.8937 (m-80) REVERT: B 121 THR cc_start: 0.9418 (p) cc_final: 0.9138 (t) REVERT: B 131 ASP cc_start: 0.8612 (m-30) cc_final: 0.8377 (m-30) REVERT: B 133 GLU cc_start: 0.9447 (mt-10) cc_final: 0.9183 (pt0) REVERT: B 159 MET cc_start: 0.8666 (tpp) cc_final: 0.8376 (tpp) REVERT: B 161 PHE cc_start: 0.8573 (m-10) cc_final: 0.8143 (m-10) REVERT: B 215 LYS cc_start: 0.9382 (mttt) cc_final: 0.9084 (mmmt) REVERT: B 231 ASP cc_start: 0.9405 (m-30) cc_final: 0.9003 (m-30) REVERT: B 235 ASN cc_start: 0.9483 (m-40) cc_final: 0.9210 (m-40) REVERT: B 242 MET cc_start: 0.9214 (mmt) cc_final: 0.8925 (mmm) REVERT: B 261 LEU cc_start: 0.9149 (mt) cc_final: 0.8880 (tp) REVERT: B 284 ILE cc_start: 0.9633 (mp) cc_final: 0.9415 (mp) REVERT: B 288 PHE cc_start: 0.9519 (m-10) cc_final: 0.9300 (m-10) REVERT: B 291 MET cc_start: 0.9392 (ttt) cc_final: 0.8599 (tpt) REVERT: B 296 ARG cc_start: 0.5429 (mtt180) cc_final: 0.5140 (ttm170) REVERT: B 312 MET cc_start: 0.8848 (mmm) cc_final: 0.8363 (mmm) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.0587 time to fit residues: 20.0853 Evaluate side-chains 193 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 27 optimal weight: 0.9980 chunk 92 optimal weight: 40.0000 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 40.0000 chunk 76 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.083689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.064032 restraints weight = 28889.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.066076 restraints weight = 19712.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067669 restraints weight = 14588.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.068911 restraints weight = 11366.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.069865 restraints weight = 9224.786| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7090 Z= 0.140 Angle : 0.646 13.196 9661 Z= 0.340 Chirality : 0.044 0.158 1212 Planarity : 0.004 0.079 1249 Dihedral : 3.931 21.751 1106 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.27), residues: 1058 helix: 1.52 (0.19), residues: 725 sheet: -1.55 (1.44), residues: 14 loop : -1.96 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 238 TYR 0.006 0.001 TYR A 87 PHE 0.035 0.002 PHE B 43 TRP 0.021 0.002 TRP A 91 HIS 0.001 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7090) covalent geometry : angle 0.64606 ( 9661) hydrogen bonds : bond 0.04439 ( 568) hydrogen bonds : angle 4.61806 ( 1677) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9521 (mt) cc_final: 0.9218 (mt) REVERT: A 75 MET cc_start: 0.9429 (mmm) cc_final: 0.9038 (mmm) REVERT: A 98 MET cc_start: 0.8941 (mmm) cc_final: 0.8602 (tpp) REVERT: A 105 PHE cc_start: 0.9439 (m-10) cc_final: 0.8922 (m-80) REVERT: A 107 HIS cc_start: 0.8580 (m-70) cc_final: 0.8214 (m170) REVERT: A 131 ASP cc_start: 0.8660 (m-30) cc_final: 0.8250 (m-30) REVERT: A 133 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8888 (pt0) REVERT: A 161 PHE cc_start: 0.8638 (m-10) cc_final: 0.8159 (m-10) REVERT: A 291 MET cc_start: 0.9102 (mmm) cc_final: 0.8764 (tpt) REVERT: A 296 ARG cc_start: 0.5822 (mtt180) cc_final: 0.5417 (ttt180) REVERT: A 303 ASN cc_start: 0.9385 (m110) cc_final: 0.9148 (p0) REVERT: A 305 ASN cc_start: 0.8652 (t0) cc_final: 0.8409 (t0) REVERT: A 312 MET cc_start: 0.8959 (mmm) cc_final: 0.8305 (mtt) REVERT: B 54 ASP cc_start: 0.9334 (m-30) cc_final: 0.8809 (t0) REVERT: B 67 MET cc_start: 0.9309 (mpp) cc_final: 0.9027 (mpp) REVERT: B 75 MET cc_start: 0.9473 (mmm) cc_final: 0.9021 (mmm) REVERT: B 105 PHE cc_start: 0.9421 (m-10) cc_final: 0.8963 (m-80) REVERT: B 121 THR cc_start: 0.9431 (p) cc_final: 0.9175 (t) REVERT: B 133 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9158 (pt0) REVERT: B 156 LEU cc_start: 0.9477 (mt) cc_final: 0.9148 (pp) REVERT: B 231 ASP cc_start: 0.9417 (m-30) cc_final: 0.9061 (m-30) REVERT: B 242 MET cc_start: 0.9139 (mmt) cc_final: 0.8872 (mmm) REVERT: B 261 LEU cc_start: 0.9038 (mt) cc_final: 0.8783 (tp) REVERT: B 267 LEU cc_start: 0.9417 (mt) cc_final: 0.9203 (mp) REVERT: B 288 PHE cc_start: 0.9481 (m-10) cc_final: 0.9271 (m-10) REVERT: B 291 MET cc_start: 0.9385 (ttt) cc_final: 0.8586 (tpt) REVERT: B 294 LEU cc_start: 0.9546 (mt) cc_final: 0.9307 (mt) REVERT: B 296 ARG cc_start: 0.5409 (mtt180) cc_final: 0.4983 (ttm170) REVERT: B 312 MET cc_start: 0.8812 (mmm) cc_final: 0.7854 (mmm) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.0589 time to fit residues: 21.2017 Evaluate side-chains 204 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 40.0000 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.081969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.063265 restraints weight = 29266.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.065314 restraints weight = 19786.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.066874 restraints weight = 14539.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068113 restraints weight = 11307.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.069062 restraints weight = 9162.958| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7090 Z= 0.150 Angle : 0.675 13.222 9661 Z= 0.348 Chirality : 0.045 0.280 1212 Planarity : 0.004 0.071 1249 Dihedral : 3.928 20.641 1106 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 1058 helix: 1.43 (0.20), residues: 722 sheet: -1.27 (1.17), residues: 24 loop : -1.83 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 238 TYR 0.008 0.001 TYR B 162 PHE 0.017 0.002 PHE A 265 TRP 0.017 0.002 TRP B 91 HIS 0.002 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7090) covalent geometry : angle 0.67512 ( 9661) hydrogen bonds : bond 0.04425 ( 568) hydrogen bonds : angle 4.66239 ( 1677) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9531 (mt) cc_final: 0.9239 (mt) REVERT: A 75 MET cc_start: 0.9461 (mmm) cc_final: 0.9068 (mmm) REVERT: A 98 MET cc_start: 0.8998 (mmm) cc_final: 0.8656 (tpp) REVERT: A 105 PHE cc_start: 0.9497 (m-10) cc_final: 0.9018 (m-80) REVERT: A 107 HIS cc_start: 0.8563 (m-70) cc_final: 0.8250 (m170) REVERT: A 131 ASP cc_start: 0.8676 (m-30) cc_final: 0.8457 (m-30) REVERT: A 133 GLU cc_start: 0.9384 (mt-10) cc_final: 0.8902 (pt0) REVERT: A 161 PHE cc_start: 0.8600 (m-10) cc_final: 0.8190 (m-10) REVERT: A 211 LEU cc_start: 0.9769 (mt) cc_final: 0.9543 (mt) REVERT: A 223 GLN cc_start: 0.9111 (mp-120) cc_final: 0.8764 (mp10) REVERT: A 242 MET cc_start: 0.9311 (mmp) cc_final: 0.9080 (mmm) REVERT: A 291 MET cc_start: 0.9176 (mmm) cc_final: 0.8799 (tpt) REVERT: A 296 ARG cc_start: 0.5718 (mtt180) cc_final: 0.5102 (ttt180) REVERT: A 303 ASN cc_start: 0.9433 (m110) cc_final: 0.9176 (p0) REVERT: A 312 MET cc_start: 0.8949 (mmm) cc_final: 0.8305 (mtt) REVERT: B 24 LYS cc_start: 0.7632 (tttt) cc_final: 0.7220 (tttt) REVERT: B 54 ASP cc_start: 0.9351 (m-30) cc_final: 0.8909 (t0) REVERT: B 75 MET cc_start: 0.9477 (mmm) cc_final: 0.9123 (mmm) REVERT: B 98 MET cc_start: 0.9335 (ttt) cc_final: 0.8426 (ttt) REVERT: B 102 ARG cc_start: 0.9024 (ttm170) cc_final: 0.8597 (ttm170) REVERT: B 105 PHE cc_start: 0.9448 (m-10) cc_final: 0.9011 (m-80) REVERT: B 108 MET cc_start: 0.9103 (mtm) cc_final: 0.8752 (mtm) REVERT: B 121 THR cc_start: 0.9407 (p) cc_final: 0.9090 (t) REVERT: B 133 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9133 (pt0) REVERT: B 242 MET cc_start: 0.9204 (mmt) cc_final: 0.8969 (mmm) REVERT: B 261 LEU cc_start: 0.9093 (mt) cc_final: 0.8846 (tp) REVERT: B 267 LEU cc_start: 0.9457 (mt) cc_final: 0.9220 (mp) REVERT: B 284 ILE cc_start: 0.9645 (mp) cc_final: 0.9442 (mp) REVERT: B 288 PHE cc_start: 0.9491 (m-10) cc_final: 0.9290 (m-10) REVERT: B 291 MET cc_start: 0.9410 (ttt) cc_final: 0.8659 (tpt) REVERT: B 312 MET cc_start: 0.8890 (mmm) cc_final: 0.8303 (mmm) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.0607 time to fit residues: 19.7957 Evaluate side-chains 198 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 30.0000 chunk 105 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 44 optimal weight: 0.0470 chunk 45 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.083704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.063749 restraints weight = 29607.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065848 restraints weight = 20126.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.067419 restraints weight = 14819.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068653 restraints weight = 11558.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069364 restraints weight = 9429.824| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7090 Z= 0.148 Angle : 0.664 10.851 9661 Z= 0.350 Chirality : 0.045 0.217 1212 Planarity : 0.004 0.067 1249 Dihedral : 3.926 20.024 1106 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.27), residues: 1058 helix: 1.46 (0.20), residues: 724 sheet: -1.30 (1.13), residues: 24 loop : -1.80 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 148 TYR 0.012 0.001 TYR A 87 PHE 0.035 0.002 PHE A 308 TRP 0.013 0.002 TRP B 91 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7090) covalent geometry : angle 0.66390 ( 9661) hydrogen bonds : bond 0.04409 ( 568) hydrogen bonds : angle 4.63318 ( 1677) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9507 (mt) cc_final: 0.9191 (mt) REVERT: A 75 MET cc_start: 0.9419 (mmm) cc_final: 0.8866 (mmm) REVERT: A 98 MET cc_start: 0.8972 (mmm) cc_final: 0.8672 (tpp) REVERT: A 100 MET cc_start: 0.9590 (mmm) cc_final: 0.9291 (mmp) REVERT: A 105 PHE cc_start: 0.9482 (m-10) cc_final: 0.8994 (m-80) REVERT: A 131 ASP cc_start: 0.8564 (m-30) cc_final: 0.8301 (m-30) REVERT: A 133 GLU cc_start: 0.9402 (mt-10) cc_final: 0.8894 (pt0) REVERT: A 161 PHE cc_start: 0.8570 (m-10) cc_final: 0.8139 (m-10) REVERT: A 208 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8997 (tm-30) REVERT: A 212 LYS cc_start: 0.9404 (mttt) cc_final: 0.8840 (pttp) REVERT: A 223 GLN cc_start: 0.9074 (mp-120) cc_final: 0.8838 (mp10) REVERT: A 231 ASP cc_start: 0.9203 (m-30) cc_final: 0.8919 (m-30) REVERT: A 242 MET cc_start: 0.9293 (mmp) cc_final: 0.9074 (mmm) REVERT: A 288 PHE cc_start: 0.9461 (m-10) cc_final: 0.9235 (m-10) REVERT: A 291 MET cc_start: 0.9162 (mmm) cc_final: 0.8745 (tpt) REVERT: A 303 ASN cc_start: 0.9407 (m110) cc_final: 0.9179 (p0) REVERT: A 312 MET cc_start: 0.8909 (mmm) cc_final: 0.8365 (mtt) REVERT: B 24 LYS cc_start: 0.7586 (tttt) cc_final: 0.7051 (tttt) REVERT: B 54 ASP cc_start: 0.9347 (m-30) cc_final: 0.8873 (t0) REVERT: B 75 MET cc_start: 0.9458 (mmm) cc_final: 0.9117 (mmm) REVERT: B 98 MET cc_start: 0.9338 (ttt) cc_final: 0.9121 (ttt) REVERT: B 105 PHE cc_start: 0.9370 (m-10) cc_final: 0.8972 (m-80) REVERT: B 133 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9132 (pt0) REVERT: B 231 ASP cc_start: 0.9479 (m-30) cc_final: 0.8879 (m-30) REVERT: B 235 ASN cc_start: 0.9593 (m-40) cc_final: 0.9263 (m-40) REVERT: B 242 MET cc_start: 0.9167 (mmt) cc_final: 0.8948 (mmm) REVERT: B 261 LEU cc_start: 0.9057 (mt) cc_final: 0.8779 (tp) REVERT: B 291 MET cc_start: 0.9374 (ttt) cc_final: 0.8618 (tpt) REVERT: B 312 MET cc_start: 0.8844 (mmm) cc_final: 0.7998 (mmm) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.0608 time to fit residues: 20.0694 Evaluate side-chains 186 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.080200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.061185 restraints weight = 29620.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.063136 restraints weight = 20083.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064578 restraints weight = 14760.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.065702 restraints weight = 11566.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066577 restraints weight = 9447.979| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7090 Z= 0.203 Angle : 0.710 8.912 9661 Z= 0.381 Chirality : 0.046 0.216 1212 Planarity : 0.005 0.061 1249 Dihedral : 4.156 25.595 1106 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.18 % Allowed : 0.73 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.27), residues: 1058 helix: 1.32 (0.20), residues: 723 sheet: -1.28 (0.93), residues: 34 loop : -1.75 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.015 0.001 TYR B 162 PHE 0.035 0.002 PHE B 116 TRP 0.021 0.002 TRP B 91 HIS 0.005 0.002 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 7090) covalent geometry : angle 0.71048 ( 9661) hydrogen bonds : bond 0.04759 ( 568) hydrogen bonds : angle 4.79253 ( 1677) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9524 (mt) cc_final: 0.9226 (mt) REVERT: A 74 LEU cc_start: 0.9647 (mt) cc_final: 0.9433 (mt) REVERT: A 75 MET cc_start: 0.9470 (mmm) cc_final: 0.8914 (mmm) REVERT: A 98 MET cc_start: 0.9048 (mmm) cc_final: 0.8570 (tpp) REVERT: A 105 PHE cc_start: 0.9481 (m-10) cc_final: 0.9026 (m-80) REVERT: A 131 ASP cc_start: 0.8734 (m-30) cc_final: 0.8497 (m-30) REVERT: A 133 GLU cc_start: 0.9400 (mt-10) cc_final: 0.8919 (pt0) REVERT: A 159 MET cc_start: 0.9393 (tpp) cc_final: 0.9131 (tpp) REVERT: A 161 PHE cc_start: 0.8699 (m-10) cc_final: 0.8319 (m-10) REVERT: A 208 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8997 (tm-30) REVERT: A 212 LYS cc_start: 0.9438 (mttt) cc_final: 0.8868 (pttp) REVERT: A 231 ASP cc_start: 0.9289 (m-30) cc_final: 0.8950 (m-30) REVERT: A 242 MET cc_start: 0.9313 (mmp) cc_final: 0.9108 (mmm) REVERT: A 291 MET cc_start: 0.9273 (mmm) cc_final: 0.8857 (tpt) REVERT: A 312 MET cc_start: 0.9022 (mmm) cc_final: 0.8320 (mtt) REVERT: B 24 LYS cc_start: 0.7713 (tttt) cc_final: 0.7281 (tttt) REVERT: B 75 MET cc_start: 0.9525 (mmm) cc_final: 0.9227 (mmm) REVERT: B 98 MET cc_start: 0.9377 (ttt) cc_final: 0.9090 (ttt) REVERT: B 105 PHE cc_start: 0.9402 (m-10) cc_final: 0.8956 (m-80) REVERT: B 108 MET cc_start: 0.9163 (mtm) cc_final: 0.8813 (mtm) REVERT: B 127 ARG cc_start: 0.9207 (tpp-160) cc_final: 0.8898 (tpp-160) REVERT: B 131 ASP cc_start: 0.8669 (m-30) cc_final: 0.8416 (m-30) REVERT: B 133 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9120 (pt0) REVERT: B 231 ASP cc_start: 0.9494 (m-30) cc_final: 0.8955 (m-30) REVERT: B 235 ASN cc_start: 0.9569 (m-40) cc_final: 0.9312 (m-40) REVERT: B 242 MET cc_start: 0.9251 (mmt) cc_final: 0.9004 (mmm) REVERT: B 261 LEU cc_start: 0.9115 (mt) cc_final: 0.8879 (tp) REVERT: B 284 ILE cc_start: 0.9676 (mp) cc_final: 0.9406 (mp) REVERT: B 288 PHE cc_start: 0.9511 (m-10) cc_final: 0.9308 (m-10) REVERT: B 291 MET cc_start: 0.9428 (ttt) cc_final: 0.8708 (tpt) REVERT: B 312 MET cc_start: 0.9056 (mmm) cc_final: 0.8455 (mmm) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.0625 time to fit residues: 20.1576 Evaluate side-chains 185 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 50.0000 chunk 80 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 41 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 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 = 0.3543 r_free = 0.3543 target = 0.083260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.063704 restraints weight = 28463.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065688 restraints weight = 19430.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067242 restraints weight = 14398.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068410 restraints weight = 11224.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.069309 restraints weight = 9208.101| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7090 Z= 0.151 Angle : 0.722 12.302 9661 Z= 0.373 Chirality : 0.045 0.201 1212 Planarity : 0.004 0.063 1249 Dihedral : 4.072 21.499 1106 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.27), residues: 1058 helix: 1.39 (0.20), residues: 727 sheet: -1.17 (0.94), residues: 34 loop : -1.75 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.007 0.001 TYR B 162 PHE 0.036 0.002 PHE A 288 TRP 0.016 0.002 TRP B 91 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7090) covalent geometry : angle 0.72193 ( 9661) hydrogen bonds : bond 0.04546 ( 568) hydrogen bonds : angle 4.75885 ( 1677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1138.00 seconds wall clock time: 20 minutes 24.70 seconds (1224.70 seconds total)