Starting phenix.real_space_refine on Thu Jul 2 09:28:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zt6_14955/07_2026/7zt6_14955.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zt6_14955/07_2026/7zt6_14955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zt6_14955/07_2026/7zt6_14955.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zt6_14955/07_2026/7zt6_14955.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zt6_14955/07_2026/7zt6_14955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zt6_14955/07_2026/7zt6_14955.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zt6_14955/07_2026/7zt6_14955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zt6_14955/07_2026/7zt6_14955.map" } resolution = 3.5 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= 0.001 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 38 5.16 5 C 5175 2.51 5 N 1363 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8073 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3863 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 27, 'TRANS': 473} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 4, 'ASP:plan': 10, 'ARG:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4174 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 26, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.34, per 1000 atoms: 0.17 Number of scatterers: 8073 At special positions: 0 Unit cell: (88.02, 92.584, 132.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 6 15.00 O 1491 8.00 N 1363 7.00 C 5175 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: 0.58 Conformation dependent library (CDL) restraints added in 286.1 milliseconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 36.9% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.574A pdb=" N PHE A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 78 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 216 through 220 removed outlier: 4.117A pdb=" N ASP A 219 " --> pdb=" O PHE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.755A pdb=" N THR A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 330 through 338 removed outlier: 4.044A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.598A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 87 through 96 Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 199 through 217 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.883A pdb=" N LEU B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.982A pdb=" N ARG B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 4.872A pdb=" N VAL B 236 " --> pdb=" O LYS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.981A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.600A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 537 removed outlier: 3.911A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.308A pdb=" N SER A 37 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N MET A 167 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A 39 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE A 169 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 41 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 168 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.536A pdb=" N TYR A 369 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 409 " --> pdb=" O TYR A 400 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 349 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.708A pdb=" N ILE B 540 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.272A pdb=" N HIS B 80 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU B 58 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N HIS B 82 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU B 56 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 53 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 10 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA B 9 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLU B 133 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 11 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE B 135 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N CYS B 13 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 253 removed outlier: 3.587A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 390 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE B 345 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 392 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 467 removed outlier: 4.481A pdb=" N THR B 472 " --> pdb=" O ASP B 467 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 984 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: 1.07 Time building geometry restraints manager: 0.73 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: 2576 1.34 - 1.46: 1274 1.46 - 1.57: 4319 1.57 - 1.69: 6 1.69 - 1.81: 64 Bond restraints: 8239 Sorted by residual: bond pdb=" O12 IHP A 701 " pdb=" P2 IHP A 701 " ideal model delta sigma weight residual 1.675 1.595 0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" O15 IHP A 701 " pdb=" P5 IHP A 701 " ideal model delta sigma weight residual 1.675 1.598 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" O16 IHP A 701 " pdb=" P6 IHP A 701 " ideal model delta sigma weight residual 1.672 1.603 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C MET A 446 " pdb=" N PRO A 447 " ideal model delta sigma weight residual 1.334 1.371 -0.037 1.11e-02 8.12e+03 1.11e+01 bond pdb=" N ARG A 444 " pdb=" CA ARG A 444 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.18e-02 7.18e+03 9.56e+00 ... (remaining 8234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 10808 1.73 - 3.45: 276 3.45 - 5.18: 46 5.18 - 6.91: 14 6.91 - 8.64: 5 Bond angle restraints: 11149 Sorted by residual: angle pdb=" N LYS A 358 " pdb=" CA LYS A 358 " pdb=" C LYS A 358 " ideal model delta sigma weight residual 113.41 108.08 5.33 1.22e+00 6.72e-01 1.91e+01 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 111.88 107.28 4.60 1.06e+00 8.90e-01 1.89e+01 angle pdb=" N LYS B 481 " pdb=" CA LYS B 481 " pdb=" C LYS B 481 " ideal model delta sigma weight residual 113.23 108.09 5.14 1.24e+00 6.50e-01 1.72e+01 angle pdb=" CA ILE B 482 " pdb=" C ILE B 482 " pdb=" O ILE B 482 " ideal model delta sigma weight residual 119.71 115.91 3.80 9.30e-01 1.16e+00 1.67e+01 angle pdb=" CA ILE B 482 " pdb=" C ILE B 482 " pdb=" N PRO B 483 " ideal model delta sigma weight residual 119.15 123.56 -4.41 1.20e+00 6.94e-01 1.35e+01 ... (remaining 11144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4607 17.56 - 35.12: 350 35.12 - 52.69: 61 52.69 - 70.25: 16 70.25 - 87.81: 6 Dihedral angle restraints: 5040 sinusoidal: 2015 harmonic: 3025 Sorted by residual: dihedral pdb=" CA GLU B 199 " pdb=" C GLU B 199 " pdb=" N GLN B 200 " pdb=" CA GLN B 200 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA MET B 14 " pdb=" C MET B 14 " pdb=" N ASP B 15 " pdb=" CA ASP B 15 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LYS A 510 " pdb=" C LYS A 510 " pdb=" N VAL A 511 " pdb=" CA VAL A 511 " ideal model delta harmonic sigma weight residual -180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1126 0.074 - 0.148: 134 0.148 - 0.222: 5 0.222 - 0.295: 1 0.295 - 0.369: 1 Chirality restraints: 1267 Sorted by residual: chirality pdb=" C1 IHP A 701 " pdb=" C2 IHP A 701 " pdb=" C6 IHP A 701 " pdb=" O11 IHP A 701 " both_signs ideal model delta sigma weight residual False 2.32 2.69 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C5 IHP A 701 " pdb=" C4 IHP A 701 " pdb=" C6 IHP A 701 " pdb=" O15 IHP A 701 " both_signs ideal model delta sigma weight residual False -2.42 -2.66 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C3 IHP A 701 " pdb=" C2 IHP A 701 " pdb=" C4 IHP A 701 " pdb=" O13 IHP A 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.55 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1264 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 71 " 0.014 2.00e-02 2.50e+03 1.12e-02 2.52e+00 pdb=" CG TYR A 71 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 71 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 71 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 71 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 71 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 71 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 161 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.55e+00 pdb=" C MET A 161 " -0.022 2.00e-02 2.50e+03 pdb=" O MET A 161 " 0.008 2.00e-02 2.50e+03 pdb=" N SER A 162 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 199 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C GLU B 199 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU B 199 " -0.007 2.00e-02 2.50e+03 pdb=" N GLN B 200 " -0.007 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 970 2.74 - 3.28: 8723 3.28 - 3.82: 13693 3.82 - 4.36: 15737 4.36 - 4.90: 26381 Nonbonded interactions: 65504 Sorted by model distance: nonbonded pdb=" OD1 ASP B 467 " pdb=" OG1 THR B 472 " model vdw 2.203 3.040 nonbonded pdb=" O ASP B 116 " pdb=" ND1 HIS B 120 " model vdw 2.221 3.120 nonbonded pdb=" OG SER B 348 " pdb=" OD2 ASP B 388 " model vdw 2.229 3.040 nonbonded pdb=" OE2 GLU A 371 " pdb=" OG SER A 373 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR A 361 " pdb=" O GLY B 358 " model vdw 2.236 3.040 ... (remaining 65499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.340 Find NCS groups from input model: 0.030 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 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 : 0.006 0.080 8239 Z= 0.308 Angle : 0.707 8.637 11149 Z= 0.389 Chirality : 0.045 0.369 1267 Planarity : 0.003 0.027 1424 Dihedral : 13.247 87.810 3070 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.70 % Allowed : 0.35 % Favored : 98.95 % 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: 0.29 (0.27), residues: 1025 helix: 1.84 (0.29), residues: 328 sheet: -0.65 (0.39), residues: 167 loop : -0.55 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 81 TYR 0.028 0.002 TYR A 71 PHE 0.015 0.001 PHE B 135 TRP 0.011 0.001 TRP A 148 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.31 ( 8239) covalent geometry : angle 0.70655 / 0.39 (11149) hydrogen bonds : bond 0.17604 / 12.25 ( 349) hydrogen bonds : angle 7.36730 / 5.41 ( 984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.254 Fit side-chains REVERT: A 48 MET cc_start: 0.9190 (mmt) cc_final: 0.8882 (mmm) REVERT: A 62 MET cc_start: 0.9366 (mmp) cc_final: 0.9099 (mmm) REVERT: A 348 MET cc_start: 0.8698 (mpp) cc_final: 0.8204 (mpp) REVERT: A 514 MET cc_start: 0.9723 (ptp) cc_final: 0.9435 (pmm) REVERT: B 13 CYS cc_start: 0.9172 (t) cc_final: 0.8795 (t) REVERT: B 14 MET cc_start: 0.9160 (tpp) cc_final: 0.8933 (tpp) REVERT: B 115 MET cc_start: 0.7604 (ppp) cc_final: 0.7173 (ppp) REVERT: B 479 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8860 (t) outliers start: 6 outliers final: 1 residues processed: 46 average time/residue: 0.0633 time to fit residues: 4.4449 Evaluate side-chains 35 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 479 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.034088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.023970 restraints weight = 58757.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.024895 restraints weight = 31348.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.025550 restraints weight = 21350.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.025995 restraints weight = 16533.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.026298 restraints weight = 14005.432| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8239 Z= 0.124 Angle : 0.567 6.891 11149 Z= 0.286 Chirality : 0.042 0.143 1267 Planarity : 0.003 0.035 1424 Dihedral : 4.901 51.922 1107 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.47 % Allowed : 5.47 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.55 (0.27), residues: 1025 helix: 1.96 (0.28), residues: 339 sheet: -0.13 (0.39), residues: 174 loop : -0.52 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 488 TYR 0.017 0.001 TYR A 71 PHE 0.011 0.001 PHE B 135 TRP 0.009 0.001 TRP A 148 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8239) covalent geometry : angle 0.56709 / 0.29 (11149) hydrogen bonds : bond 0.03881 / 2.60 ( 349) hydrogen bonds : angle 5.79446 / 4.14 ( 984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.187 Fit side-chains REVERT: A 167 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9104 (mtt) REVERT: A 346 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8468 (ptp) REVERT: A 348 MET cc_start: 0.8644 (mpp) cc_final: 0.8354 (mpp) REVERT: A 398 CYS cc_start: 0.9008 (m) cc_final: 0.8614 (t) REVERT: B 13 CYS cc_start: 0.9313 (t) cc_final: 0.9111 (t) REVERT: B 115 MET cc_start: 0.7867 (ppp) cc_final: 0.7465 (ppp) REVERT: B 479 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9104 (t) outliers start: 4 outliers final: 1 residues processed: 40 average time/residue: 0.0525 time to fit residues: 3.4735 Evaluate side-chains 37 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 479 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 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 = 0.3060 r_free = 0.3060 target = 0.034877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.025133 restraints weight = 59979.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.026049 restraints weight = 30800.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.026646 restraints weight = 20500.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.027076 restraints weight = 15872.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.027316 restraints weight = 13355.055| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8239 Z= 0.285 Angle : 0.623 7.899 11149 Z= 0.314 Chirality : 0.040 0.133 1267 Planarity : 0.003 0.029 1424 Dihedral : 4.788 45.655 1107 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.93 % Allowed : 8.84 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.27), residues: 1025 helix: 1.92 (0.28), residues: 345 sheet: -0.37 (0.39), residues: 181 loop : -0.54 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 232 TYR 0.013 0.002 TYR A 71 PHE 0.009 0.001 PHE A 49 TRP 0.007 0.001 TRP A 148 HIS 0.005 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.28 ( 8239) covalent geometry : angle 0.62275 / 0.31 (11149) hydrogen bonds : bond 0.03673 / 2.45 ( 349) hydrogen bonds : angle 5.66118 / 4.05 ( 984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.300 Fit side-chains REVERT: A 62 MET cc_start: 0.9275 (mmm) cc_final: 0.8985 (mmm) REVERT: A 203 MET cc_start: 0.9632 (mmt) cc_final: 0.8903 (mmm) REVERT: A 346 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8235 (ptp) REVERT: A 348 MET cc_start: 0.8682 (mpp) cc_final: 0.8193 (mpp) REVERT: A 398 CYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8605 (t) REVERT: B 212 MET cc_start: 0.9363 (tpp) cc_final: 0.9157 (tpp) REVERT: B 357 MET cc_start: 0.8985 (mmm) cc_final: 0.8574 (tpp) REVERT: B 479 THR cc_start: 0.9524 (OUTLIER) cc_final: 0.9312 (t) outliers start: 8 outliers final: 3 residues processed: 39 average time/residue: 0.0603 time to fit residues: 3.8776 Evaluate side-chains 37 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 479 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 80 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 GLN ** A 416 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 = 0.3058 r_free = 0.3058 target = 0.034900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.025301 restraints weight = 59916.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.026209 restraints weight = 30298.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.026853 restraints weight = 20132.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.027240 restraints weight = 15281.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.027550 restraints weight = 12942.016| |-----------------------------------------------------------------------------| r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8239 Z= 0.200 Angle : 0.558 8.825 11149 Z= 0.281 Chirality : 0.040 0.135 1267 Planarity : 0.003 0.024 1424 Dihedral : 4.579 37.455 1107 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.81 % Allowed : 10.35 % Favored : 88.84 % 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: 0.55 (0.27), residues: 1025 helix: 2.00 (0.28), residues: 347 sheet: -0.29 (0.41), residues: 167 loop : -0.53 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 497 TYR 0.010 0.001 TYR A 71 PHE 0.008 0.001 PHE A 49 TRP 0.008 0.001 TRP A 148 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 ( 8239) covalent geometry : angle 0.55768 / 0.28 (11149) hydrogen bonds : bond 0.03316 / 2.19 ( 349) hydrogen bonds : angle 5.46428 / 3.90 ( 984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.213 Fit side-chains REVERT: A 62 MET cc_start: 0.9285 (mmm) cc_final: 0.8918 (mmm) REVERT: A 203 MET cc_start: 0.9617 (mmt) cc_final: 0.8903 (mmm) REVERT: A 346 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8152 (ptp) REVERT: A 348 MET cc_start: 0.8566 (mpp) cc_final: 0.8317 (mpp) REVERT: A 398 CYS cc_start: 0.8972 (m) cc_final: 0.8546 (t) REVERT: B 115 MET cc_start: 0.7616 (ppp) cc_final: 0.7167 (ppp) REVERT: B 212 MET cc_start: 0.9392 (tpp) cc_final: 0.9119 (tpp) REVERT: B 357 MET cc_start: 0.8997 (mmm) cc_final: 0.8572 (tpp) REVERT: B 479 THR cc_start: 0.9501 (OUTLIER) cc_final: 0.9295 (t) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.0549 time to fit residues: 3.6089 Evaluate side-chains 38 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 479 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 52 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 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 = 0.3200 r_free = 0.3200 target = 0.046237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.038705 restraints weight = 72635.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.039676 restraints weight = 31832.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.040336 restraints weight = 18849.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.040672 restraints weight = 13306.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.041017 restraints weight = 10962.459| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8239 Z= 0.234 Angle : 0.582 7.294 11149 Z= 0.292 Chirality : 0.040 0.132 1267 Planarity : 0.003 0.024 1424 Dihedral : 4.520 29.343 1107 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.16 % Allowed : 11.63 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1025 helix: 2.00 (0.28), residues: 347 sheet: -0.33 (0.40), residues: 171 loop : -0.50 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.011 0.001 TYR A 322 PHE 0.007 0.001 PHE A 487 TRP 0.010 0.001 TRP A 148 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 ( 8239) covalent geometry : angle 0.58203 / 0.29 (11149) hydrogen bonds : bond 0.03291 / 2.18 ( 349) hydrogen bonds : angle 5.43755 / 3.89 ( 984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.256 Fit side-chains REVERT: A 48 MET cc_start: 0.8922 (mmm) cc_final: 0.8391 (mmt) REVERT: A 62 MET cc_start: 0.9250 (mmm) cc_final: 0.8824 (mmm) REVERT: A 203 MET cc_start: 0.9484 (mmt) cc_final: 0.8773 (mmm) REVERT: A 348 MET cc_start: 0.8542 (mpp) cc_final: 0.8113 (mpp) REVERT: A 398 CYS cc_start: 0.8901 (m) cc_final: 0.8488 (t) REVERT: B 212 MET cc_start: 0.9255 (tpp) cc_final: 0.8973 (tpp) REVERT: B 357 MET cc_start: 0.8924 (mmm) cc_final: 0.8547 (tpp) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.0576 time to fit residues: 4.0262 Evaluate side-chains 39 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 351 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 46 optimal weight: 0.0870 chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.024604 restraints weight = 58501.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.025521 restraints weight = 30281.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.026147 restraints weight = 20250.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.026576 restraints weight = 15613.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.026863 restraints weight = 13141.375| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8239 Z= 0.116 Angle : 0.540 11.405 11149 Z= 0.264 Chirality : 0.040 0.135 1267 Planarity : 0.003 0.022 1424 Dihedral : 4.271 21.694 1106 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.40 % Allowed : 11.51 % Favored : 87.09 % 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: 0.71 (0.27), residues: 1025 helix: 2.09 (0.28), residues: 347 sheet: -0.09 (0.41), residues: 164 loop : -0.44 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 232 TYR 0.011 0.001 TYR A 88 PHE 0.008 0.001 PHE A 410 TRP 0.013 0.001 TRP A 148 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 8239) covalent geometry : angle 0.53953 / 0.26 (11149) hydrogen bonds : bond 0.03033 / 1.99 ( 349) hydrogen bonds : angle 5.28149 / 3.77 ( 984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.221 Fit side-chains REVERT: A 62 MET cc_start: 0.9314 (mmm) cc_final: 0.8830 (mmm) REVERT: A 203 MET cc_start: 0.9555 (mmt) cc_final: 0.8841 (mmm) REVERT: B 115 MET cc_start: 0.7637 (ppp) cc_final: 0.7226 (ppp) REVERT: B 212 MET cc_start: 0.9440 (tpp) cc_final: 0.9112 (tpp) REVERT: B 357 MET cc_start: 0.8939 (mmm) cc_final: 0.8509 (tpp) outliers start: 12 outliers final: 6 residues processed: 46 average time/residue: 0.0540 time to fit residues: 4.0916 Evaluate side-chains 39 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 351 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 99 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 14 optimal weight: 0.0770 chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 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 = 0.3260 r_free = 0.3260 target = 0.048800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.041345 restraints weight = 70811.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.042338 restraints weight = 30806.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.042997 restraints weight = 18022.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.043307 restraints weight = 12636.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.043654 restraints weight = 10405.343| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8239 Z= 0.090 Angle : 0.553 10.352 11149 Z= 0.269 Chirality : 0.041 0.142 1267 Planarity : 0.003 0.024 1424 Dihedral : 4.104 20.400 1106 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.70 % Allowed : 12.67 % Favored : 86.63 % 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: 0.70 (0.27), residues: 1025 helix: 1.98 (0.28), residues: 349 sheet: -0.03 (0.41), residues: 164 loop : -0.40 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.012 0.001 TYR A 88 PHE 0.010 0.001 PHE B 59 TRP 0.019 0.002 TRP A 148 HIS 0.003 0.000 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 ( 8239) covalent geometry : angle 0.55283 / 0.27 (11149) hydrogen bonds : bond 0.02861 / 1.89 ( 349) hydrogen bonds : angle 5.15068 / 3.67 ( 984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.278 Fit side-chains REVERT: A 62 MET cc_start: 0.9242 (mmm) cc_final: 0.8740 (mmm) REVERT: B 115 MET cc_start: 0.7861 (ppp) cc_final: 0.7348 (ppp) REVERT: B 212 MET cc_start: 0.9263 (tpp) cc_final: 0.8956 (tpp) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.0564 time to fit residues: 3.9977 Evaluate side-chains 36 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 12 optimal weight: 0.0770 chunk 74 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 56 optimal weight: 0.0980 chunk 97 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 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 = 0.3062 r_free = 0.3062 target = 0.035351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.025706 restraints weight = 57996.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.026665 restraints weight = 29641.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.027314 restraints weight = 19562.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.027758 restraints weight = 14947.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.028034 restraints weight = 12530.494| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8239 Z= 0.093 Angle : 0.568 9.764 11149 Z= 0.270 Chirality : 0.040 0.138 1267 Planarity : 0.003 0.024 1424 Dihedral : 3.978 19.867 1105 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.58 % Allowed : 13.26 % Favored : 86.16 % 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: 0.73 (0.27), residues: 1025 helix: 2.02 (0.28), residues: 349 sheet: -0.08 (0.41), residues: 164 loop : -0.37 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.007 0.001 TYR A 71 PHE 0.009 0.001 PHE B 59 TRP 0.019 0.001 TRP A 148 HIS 0.003 0.000 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 8239) covalent geometry : angle 0.56828 / 0.27 (11149) hydrogen bonds : bond 0.02775 / 1.82 ( 349) hydrogen bonds : angle 5.05746 / 3.61 ( 984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.330 Fit side-chains REVERT: A 48 MET cc_start: 0.8969 (mmm) cc_final: 0.8395 (mmm) REVERT: A 62 MET cc_start: 0.9318 (mmm) cc_final: 0.8812 (mmm) REVERT: B 115 MET cc_start: 0.7894 (ppp) cc_final: 0.7460 (ppp) REVERT: B 212 MET cc_start: 0.9498 (tpp) cc_final: 0.9155 (tpp) REVERT: B 357 MET cc_start: 0.8954 (mmm) cc_final: 0.8558 (ttm) outliers start: 5 outliers final: 5 residues processed: 39 average time/residue: 0.0603 time to fit residues: 3.9534 Evaluate side-chains 38 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 407 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 69 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 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 = 0.3011 r_free = 0.3011 target = 0.034559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.024901 restraints weight = 58930.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.025839 restraints weight = 30723.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.026478 restraints weight = 20493.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.026880 restraints weight = 15768.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.027125 restraints weight = 13379.772| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8239 Z= 0.124 Angle : 0.567 10.107 11149 Z= 0.271 Chirality : 0.039 0.136 1267 Planarity : 0.003 0.022 1424 Dihedral : 3.941 19.898 1105 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.70 % Allowed : 12.79 % Favored : 86.51 % 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: 0.83 (0.28), residues: 1025 helix: 2.13 (0.28), residues: 349 sheet: -0.09 (0.41), residues: 167 loop : -0.30 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.007 0.001 TYR A 322 PHE 0.008 0.001 PHE A 432 TRP 0.019 0.002 TRP A 148 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8239) covalent geometry : angle 0.56704 / 0.27 (11149) hydrogen bonds : bond 0.02796 / 1.84 ( 349) hydrogen bonds : angle 4.98393 / 3.60 ( 984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.318 Fit side-chains REVERT: A 48 MET cc_start: 0.9073 (mmm) cc_final: 0.8472 (mmm) REVERT: A 62 MET cc_start: 0.9319 (mmm) cc_final: 0.8820 (mmm) REVERT: B 58 LEU cc_start: 0.9737 (OUTLIER) cc_final: 0.9311 (tp) REVERT: B 115 MET cc_start: 0.7910 (ppp) cc_final: 0.7483 (ppp) REVERT: B 212 MET cc_start: 0.9517 (tpp) cc_final: 0.9173 (tpp) REVERT: B 357 MET cc_start: 0.8978 (mmm) cc_final: 0.8598 (ttm) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.0498 time to fit residues: 3.2239 Evaluate side-chains 38 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 407 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.045707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.038164 restraints weight = 72810.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039114 restraints weight = 32282.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.039767 restraints weight = 19306.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.040125 restraints weight = 13815.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040414 restraints weight = 11283.160| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8239 Z= 0.280 Angle : 0.678 10.661 11149 Z= 0.329 Chirality : 0.040 0.160 1267 Planarity : 0.003 0.024 1424 Dihedral : 4.252 21.856 1105 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.81 % Allowed : 12.79 % Favored : 86.40 % 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: 0.74 (0.28), residues: 1025 helix: 2.14 (0.28), residues: 345 sheet: -0.24 (0.40), residues: 173 loop : -0.36 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.018 0.001 TYR A 322 PHE 0.010 0.001 PHE A 410 TRP 0.015 0.002 TRP A 148 HIS 0.005 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.28 ( 8239) covalent geometry : angle 0.67828 / 0.33 (11149) hydrogen bonds : bond 0.03217 / 2.11 ( 349) hydrogen bonds : angle 5.23118 / 3.78 ( 984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.282 Fit side-chains REVERT: A 48 MET cc_start: 0.8914 (mmm) cc_final: 0.8550 (mmm) REVERT: A 62 MET cc_start: 0.9274 (mmm) cc_final: 0.8758 (mmm) REVERT: A 167 MET cc_start: 0.9374 (mtp) cc_final: 0.8696 (mpp) REVERT: A 398 CYS cc_start: 0.8853 (m) cc_final: 0.8564 (t) REVERT: A 514 MET cc_start: 0.9549 (ptp) cc_final: 0.9261 (pmm) REVERT: B 115 MET cc_start: 0.7740 (ppp) cc_final: 0.7243 (ppp) REVERT: B 212 MET cc_start: 0.9325 (tpp) cc_final: 0.9003 (tpp) REVERT: B 357 MET cc_start: 0.8914 (mmm) cc_final: 0.8561 (tpp) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.0645 time to fit residues: 4.1689 Evaluate side-chains 36 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 407 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 66 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 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 = 0.3213 r_free = 0.3213 target = 0.046894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.039204 restraints weight = 71244.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.040174 restraints weight = 31672.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.040835 restraints weight = 18823.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.041156 restraints weight = 13384.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041489 restraints weight = 11034.192| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8239 Z= 0.193 Angle : 0.613 10.122 11149 Z= 0.296 Chirality : 0.040 0.133 1267 Planarity : 0.003 0.023 1424 Dihedral : 4.187 21.261 1105 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.70 % Allowed : 13.37 % Favored : 85.93 % 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: 0.78 (0.28), residues: 1025 helix: 2.13 (0.28), residues: 347 sheet: -0.12 (0.41), residues: 171 loop : -0.36 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 81 TYR 0.012 0.001 TYR A 322 PHE 0.009 0.001 PHE A 211 TRP 0.017 0.002 TRP A 148 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 ( 8239) covalent geometry : angle 0.61308 / 0.30 (11149) hydrogen bonds : bond 0.03044 / 2.01 ( 349) hydrogen bonds : angle 5.14903 / 3.72 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1079.19 seconds wall clock time: 19 minutes 29.13 seconds (1169.13 seconds total)