Starting phenix.real_space_refine on Tue Sep 24 12:58:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/09_2024/7zt6_14955.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/09_2024/7zt6_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/09_2024/7zt6_14955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/09_2024/7zt6_14955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/09_2024/7zt6_14955.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/09_2024/7zt6_14955.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 4, 'GLU:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 10} 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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} 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: 5.35, per 1000 atoms: 0.66 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: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.96 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: 2.35 Time building geometry restraints manager: 2.53 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: 4641 17.56 - 35.12: 352 35.12 - 52.69: 61 52.69 - 70.25: 16 70.25 - 87.81: 6 Dihedral angle restraints: 5076 sinusoidal: 2051 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 5073 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: 1.880 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.050 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 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= 0.398 Angle : 0.707 8.637 11149 Z= 0.389 Chirality : 0.045 0.369 1267 Planarity : 0.003 0.027 1424 Dihedral : 13.206 87.810 3106 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.011 0.001 TRP A 148 HIS 0.004 0.001 HIS B 131 PHE 0.015 0.001 PHE B 135 TYR 0.028 0.002 TYR A 71 ARG 0.003 0.000 ARG B 81 *********************** 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 fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.937 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: 0.8205 (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: 0.8794 (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: 0.2037 time to fit residues: 13.9082 Evaluate side-chains 35 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 86 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8239 Z= 0.266 Angle : 0.584 7.873 11149 Z= 0.296 Chirality : 0.041 0.138 1267 Planarity : 0.003 0.036 1424 Dihedral : 5.101 51.870 1143 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.81 % Allowed : 5.93 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 1025 helix: 1.91 (0.28), residues: 339 sheet: -0.38 (0.39), residues: 181 loop : -0.52 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.004 0.001 HIS B 80 PHE 0.012 0.001 PHE B 135 TYR 0.017 0.001 TYR A 71 ARG 0.003 0.000 ARG B 81 *********************** 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 44 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.971 Fit side-chains REVERT: A 48 MET cc_start: 0.9165 (mmt) cc_final: 0.8953 (mmm) REVERT: A 62 MET cc_start: 0.9379 (mmp) cc_final: 0.9155 (mmm) REVERT: A 346 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8400 (ptp) REVERT: A 348 MET cc_start: 0.8663 (mpp) cc_final: 0.8345 (mpp) REVERT: A 398 CYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8645 (t) REVERT: B 13 CYS cc_start: 0.9320 (t) cc_final: 0.9085 (t) REVERT: B 115 MET cc_start: 0.7819 (ppp) cc_final: 0.7437 (ppp) REVERT: B 479 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9193 (t) outliers start: 7 outliers final: 1 residues processed: 39 average time/residue: 0.1533 time to fit residues: 9.9750 Evaluate side-chains 36 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 398 CYS 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 51 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.0050 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8239 Z= 0.237 Angle : 0.543 8.103 11149 Z= 0.275 Chirality : 0.040 0.136 1267 Planarity : 0.003 0.024 1424 Dihedral : 4.766 42.883 1143 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.70 % Allowed : 8.84 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 1025 helix: 1.99 (0.28), residues: 347 sheet: -0.20 (0.40), residues: 177 loop : -0.54 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 148 HIS 0.003 0.001 HIS B 131 PHE 0.008 0.001 PHE A 49 TYR 0.013 0.001 TYR A 71 ARG 0.002 0.000 ARG B 497 *********************** 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 fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.903 Fit side-chains REVERT: A 48 MET cc_start: 0.9167 (mmt) cc_final: 0.8871 (mmm) REVERT: A 62 MET cc_start: 0.9388 (mmp) cc_final: 0.9132 (mmm) REVERT: A 203 MET cc_start: 0.9655 (mmt) cc_final: 0.8945 (mmm) REVERT: A 346 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8230 (ptp) REVERT: A 348 MET cc_start: 0.8630 (mpp) cc_final: 0.8149 (mpp) REVERT: A 398 CYS cc_start: 0.9021 (m) cc_final: 0.8614 (t) REVERT: B 115 MET cc_start: 0.7911 (ppp) cc_final: 0.7464 (ppp) REVERT: B 212 MET cc_start: 0.9397 (tpp) cc_final: 0.9172 (tpp) REVERT: B 357 MET cc_start: 0.8816 (mmm) cc_final: 0.8464 (tpp) REVERT: B 479 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9256 (t) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 0.1466 time to fit residues: 10.0354 Evaluate side-chains 36 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 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 92 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8239 Z= 0.350 Angle : 0.584 7.435 11149 Z= 0.295 Chirality : 0.040 0.132 1267 Planarity : 0.003 0.026 1424 Dihedral : 4.718 34.917 1143 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.93 % Allowed : 11.16 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 1025 helix: 2.01 (0.28), residues: 347 sheet: -0.35 (0.40), residues: 171 loop : -0.50 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 148 HIS 0.005 0.001 HIS B 414 PHE 0.010 0.001 PHE B 135 TYR 0.012 0.001 TYR A 322 ARG 0.001 0.000 ARG B 497 *********************** 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 41 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 1.013 Fit side-chains REVERT: A 62 MET cc_start: 0.9420 (mmp) cc_final: 0.9137 (mmm) REVERT: A 167 MET cc_start: 0.9451 (mtp) cc_final: 0.9095 (mtt) REVERT: A 203 MET cc_start: 0.9662 (mmt) cc_final: 0.8922 (mmm) REVERT: A 346 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8117 (ptp) REVERT: A 348 MET cc_start: 0.8558 (mpp) cc_final: 0.8291 (mpp) REVERT: A 398 CYS cc_start: 0.9024 (m) cc_final: 0.8608 (t) REVERT: B 14 MET cc_start: 0.9472 (tpp) cc_final: 0.9265 (tpp) REVERT: B 212 MET cc_start: 0.9452 (tpp) cc_final: 0.9174 (tpp) REVERT: B 331 MET cc_start: 0.9072 (mmm) cc_final: 0.8862 (mmm) REVERT: B 357 MET cc_start: 0.8878 (mmm) cc_final: 0.8580 (tpp) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.1495 time to fit residues: 10.0645 Evaluate side-chains 39 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 522 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 351 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 25 optimal weight: 0.0020 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8239 Z= 0.129 Angle : 0.519 7.652 11149 Z= 0.257 Chirality : 0.040 0.139 1267 Planarity : 0.003 0.024 1424 Dihedral : 4.345 21.187 1142 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.28 % Allowed : 11.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 1025 helix: 2.25 (0.28), residues: 339 sheet: -0.05 (0.41), residues: 164 loop : -0.42 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 148 HIS 0.003 0.000 HIS B 131 PHE 0.009 0.001 PHE B 59 TYR 0.013 0.001 TYR A 88 ARG 0.005 0.000 ARG B 232 *********************** 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 49 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.9281 (mmm) cc_final: 0.8614 (mmm) REVERT: A 62 MET cc_start: 0.9409 (mmp) cc_final: 0.9114 (mmm) REVERT: A 167 MET cc_start: 0.9435 (mtp) cc_final: 0.9109 (mtt) REVERT: A 348 MET cc_start: 0.8582 (mpp) cc_final: 0.8146 (mpp) REVERT: B 115 MET cc_start: 0.7784 (ppp) cc_final: 0.7418 (ppp) REVERT: B 212 MET cc_start: 0.9466 (tpp) cc_final: 0.9143 (tpp) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 0.1544 time to fit residues: 12.2431 Evaluate side-chains 40 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 58 LEU 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 33 optimal weight: 9.9990 chunk 89 optimal weight: 0.0030 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 overall best weight: 5.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8239 Z= 0.368 Angle : 0.613 8.042 11149 Z= 0.302 Chirality : 0.040 0.132 1267 Planarity : 0.003 0.023 1424 Dihedral : 4.420 21.850 1142 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.28 % Allowed : 12.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 1025 helix: 2.13 (0.28), residues: 347 sheet: -0.28 (0.40), residues: 171 loop : -0.44 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 148 HIS 0.004 0.001 HIS B 414 PHE 0.010 0.001 PHE A 432 TYR 0.012 0.001 TYR A 322 ARG 0.006 0.000 ARG B 232 *********************** 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 44 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.969 Fit side-chains REVERT: A 62 MET cc_start: 0.9439 (mmp) cc_final: 0.9153 (mmm) REVERT: A 203 MET cc_start: 0.9613 (mmm) cc_final: 0.8847 (mmm) REVERT: A 348 MET cc_start: 0.8489 (mpp) cc_final: 0.8215 (mpp) REVERT: A 398 CYS cc_start: 0.9021 (m) cc_final: 0.8556 (t) REVERT: B 115 MET cc_start: 0.7678 (ppp) cc_final: 0.7214 (ppp) REVERT: B 212 MET cc_start: 0.9512 (tpp) cc_final: 0.9180 (tpp) REVERT: B 357 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8260 (mtp) outliers start: 11 outliers final: 6 residues processed: 43 average time/residue: 0.1509 time to fit residues: 10.6686 Evaluate side-chains 40 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 357 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 99 optimal weight: 0.0770 chunk 62 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 HIS ** B 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8239 Z= 0.162 Angle : 0.564 9.299 11149 Z= 0.273 Chirality : 0.040 0.137 1267 Planarity : 0.003 0.022 1424 Dihedral : 4.279 21.018 1142 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.93 % Allowed : 13.26 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 1025 helix: 2.12 (0.28), residues: 347 sheet: -0.06 (0.41), residues: 164 loop : -0.38 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.007 0.001 HIS B 382 PHE 0.008 0.001 PHE A 211 TYR 0.012 0.001 TYR A 88 ARG 0.005 0.000 ARG B 232 *********************** 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 fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.917 Fit side-chains REVERT: A 48 MET cc_start: 0.9123 (mmm) cc_final: 0.8504 (mmm) REVERT: A 62 MET cc_start: 0.9419 (mmp) cc_final: 0.9066 (mmm) REVERT: A 203 MET cc_start: 0.9548 (mmm) cc_final: 0.8851 (mmm) REVERT: A 348 MET cc_start: 0.8474 (mpp) cc_final: 0.8160 (mpp) REVERT: A 453 MET cc_start: 0.8956 (mmm) cc_final: 0.8701 (mmp) REVERT: B 115 MET cc_start: 0.7907 (ppp) cc_final: 0.7472 (ppp) REVERT: B 212 MET cc_start: 0.9506 (tpp) cc_final: 0.9159 (tpp) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.1541 time to fit residues: 10.5047 Evaluate side-chains 36 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 29 optimal weight: 0.0870 chunk 19 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8239 Z= 0.326 Angle : 0.610 9.743 11149 Z= 0.299 Chirality : 0.040 0.133 1267 Planarity : 0.003 0.022 1424 Dihedral : 4.349 21.463 1141 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.05 % Allowed : 13.26 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1025 helix: 2.14 (0.28), residues: 347 sheet: -0.30 (0.40), residues: 169 loop : -0.37 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 148 HIS 0.004 0.001 HIS B 414 PHE 0.010 0.001 PHE B 426 TYR 0.013 0.001 TYR A 322 ARG 0.002 0.000 ARG B 81 *********************** 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 40 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 1.012 Fit side-chains REVERT: A 62 MET cc_start: 0.9436 (mmp) cc_final: 0.9149 (mmm) REVERT: A 161 MET cc_start: 0.8008 (tmm) cc_final: 0.7789 (tmm) REVERT: A 167 MET cc_start: 0.9546 (mtp) cc_final: 0.8707 (mpp) REVERT: A 348 MET cc_start: 0.8467 (mpp) cc_final: 0.8195 (mpp) REVERT: A 398 CYS cc_start: 0.9019 (m) cc_final: 0.8570 (t) REVERT: B 115 MET cc_start: 0.7777 (ppp) cc_final: 0.7346 (ppp) REVERT: B 212 MET cc_start: 0.9535 (tpp) cc_final: 0.9188 (tpp) outliers start: 9 outliers final: 5 residues processed: 39 average time/residue: 0.1544 time to fit residues: 9.9519 Evaluate side-chains 36 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 86 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 55 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8239 Z= 0.170 Angle : 0.575 10.730 11149 Z= 0.276 Chirality : 0.040 0.136 1267 Planarity : 0.003 0.022 1424 Dihedral : 4.278 21.426 1141 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.70 % Allowed : 13.72 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 1025 helix: 2.15 (0.28), residues: 347 sheet: -0.22 (0.40), residues: 167 loop : -0.37 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 148 HIS 0.003 0.001 HIS B 131 PHE 0.009 0.001 PHE A 211 TYR 0.009 0.001 TYR A 141 ARG 0.002 0.000 ARG B 81 *********************** 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 40 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 1.061 Fit side-chains REVERT: A 48 MET cc_start: 0.9058 (mmm) cc_final: 0.8468 (mmm) REVERT: A 62 MET cc_start: 0.9420 (mmp) cc_final: 0.9121 (mmm) REVERT: A 161 MET cc_start: 0.8140 (tmm) cc_final: 0.7925 (tmm) REVERT: A 167 MET cc_start: 0.9519 (mtp) cc_final: 0.8727 (mpp) REVERT: A 348 MET cc_start: 0.8456 (mpp) cc_final: 0.8232 (mpp) REVERT: B 115 MET cc_start: 0.7895 (ppp) cc_final: 0.7480 (ppp) REVERT: B 212 MET cc_start: 0.9512 (tpp) cc_final: 0.9162 (tpp) outliers start: 6 outliers final: 6 residues processed: 40 average time/residue: 0.1597 time to fit residues: 10.6135 Evaluate side-chains 38 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 59 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8239 Z= 0.396 Angle : 0.685 12.562 11149 Z= 0.331 Chirality : 0.040 0.132 1267 Planarity : 0.003 0.028 1424 Dihedral : 4.450 21.441 1141 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.93 % Allowed : 13.72 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1025 helix: 2.10 (0.28), residues: 347 sheet: -0.23 (0.40), residues: 171 loop : -0.37 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 148 HIS 0.005 0.001 HIS B 414 PHE 0.014 0.001 PHE B 356 TYR 0.016 0.001 TYR A 322 ARG 0.002 0.000 ARG B 81 ********************** 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 fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.902 Fit side-chains REVERT: A 48 MET cc_start: 0.9135 (mmm) cc_final: 0.8477 (mmm) REVERT: A 62 MET cc_start: 0.9436 (mmp) cc_final: 0.9090 (mmm) REVERT: A 161 MET cc_start: 0.8242 (tmm) cc_final: 0.8031 (tmm) REVERT: A 167 MET cc_start: 0.9507 (mtp) cc_final: 0.8745 (mpp) REVERT: A 348 MET cc_start: 0.8524 (mpp) cc_final: 0.8119 (mpp) REVERT: A 398 CYS cc_start: 0.9048 (m) cc_final: 0.8587 (t) REVERT: B 115 MET cc_start: 0.7790 (ppp) cc_final: 0.7361 (ppp) REVERT: B 212 MET cc_start: 0.9543 (tpp) cc_final: 0.9208 (tpp) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.1472 time to fit residues: 9.5735 Evaluate side-chains 38 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 25 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3235 r_free = 0.3235 target = 0.047690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.040236 restraints weight = 70188.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.041201 restraints weight = 30808.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.041848 restraints weight = 18244.731| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8239 Z= 0.177 Angle : 0.597 10.682 11149 Z= 0.284 Chirality : 0.040 0.136 1267 Planarity : 0.003 0.022 1424 Dihedral : 4.340 22.835 1141 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.70 % Allowed : 13.95 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 1025 helix: 2.17 (0.28), residues: 347 sheet: -0.16 (0.41), residues: 167 loop : -0.37 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 148 HIS 0.003 0.001 HIS B 131 PHE 0.012 0.001 PHE A 211 TYR 0.009 0.001 TYR A 141 ARG 0.002 0.000 ARG B 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1453.54 seconds wall clock time: 27 minutes 5.79 seconds (1625.79 seconds total)