Starting phenix.real_space_refine on Thu Mar 13 11:04:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6waz_21582/03_2025/6waz_21582.cif Found real_map, /net/cci-nas-00/data/ceres_data/6waz_21582/03_2025/6waz_21582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6waz_21582/03_2025/6waz_21582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6waz_21582/03_2025/6waz_21582.map" model { file = "/net/cci-nas-00/data/ceres_data/6waz_21582/03_2025/6waz_21582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6waz_21582/03_2025/6waz_21582.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 51 5.49 5 S 8 5.16 5 C 5338 2.51 5 N 1453 2.21 5 O 1687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8537 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4222 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 512} Chain breaks: 1 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 170 Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3177 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 30, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 14, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 493 Classifications: {'RNA': 23} Modifications used: {'5*END': 1, 'rna3p_pur': 13, 'rna3p_pyr': 9} Link IDs: {'rna3p': 22} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 645 Inner-chain residues flagged as termini: ['pdbres=" G D 51 "'] Classifications: {'DNA': 2, 'RNA': 29} Modifications used: {'5*END': 2, 'rna3p_pur': 10, 'rna3p_pyr': 17} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.73, per 1000 atoms: 0.67 Number of scatterers: 8537 At special positions: 0 Unit cell: (103.88, 116.6, 110.24, 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 8 16.00 P 51 15.00 O 1687 8.00 N 1453 7.00 C 5338 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: 2.23 Conformation dependent library (CDL) restraints added in 913.7 milliseconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 37.9% alpha, 9.0% beta 26 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 removed outlier: 4.367A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.903A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.715A pdb=" N THR A 128 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 253 through 269 removed outlier: 4.039A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.283A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 383 removed outlier: 3.764A pdb=" N GLN A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.552A pdb=" N TRP A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.935A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.610A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.824A pdb=" N GLN A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.934A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 removed outlier: 6.184A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.742A pdb=" N VAL B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 155 through 175 removed outlier: 4.884A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.896A pdb=" N LYS B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.549A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 311 removed outlier: 3.564A pdb=" N LYS B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 Processing helix chain 'B' and resid 394 through 406 removed outlier: 4.094A pdb=" N TRP B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR B 405 " --> pdb=" O TRP B 401 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP B 406 " --> pdb=" O TRP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 removed outlier: 3.754A pdb=" N TYR B 427 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 108 removed outlier: 3.682A pdb=" N VAL A 189 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 328 removed outlier: 7.098A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 468 removed outlier: 3.624A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 493 " --> pdb=" O TYR A 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 48 removed outlier: 3.991A pdb=" N ILE B 132 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 144 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B 130 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 62 removed outlier: 3.680A pdb=" N PHE B 61 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 74 " --> pdb=" O PHE B 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.652A pdb=" N TYR B 188 " --> pdb=" O TYR B 181 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B 181 " --> pdb=" O TYR B 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.570A pdb=" N VAL B 189 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 107 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 234 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 351 removed outlier: 7.327A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS B 390 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.801A pdb=" N GLY B 333 " --> pdb=" O GLN B 336 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1771 1.33 - 1.45: 2201 1.45 - 1.57: 4786 1.57 - 1.69: 102 1.69 - 1.81: 13 Bond restraints: 8873 Sorted by residual: bond pdb=" CB THR B 131 " pdb=" CG2 THR B 131 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.50e+00 bond pdb=" CG GLU A 194 " pdb=" CD GLU A 194 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.36e+00 bond pdb=" CG1 ILE B 380 " pdb=" CD1 ILE B 380 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.89e+00 bond pdb=" CG ASP A 86 " pdb=" OD2 ASP A 86 " ideal model delta sigma weight residual 1.249 1.217 0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" CB THR A 216 " pdb=" CG2 THR A 216 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 ... (remaining 8868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 11809 1.67 - 3.33: 442 3.33 - 5.00: 90 5.00 - 6.66: 19 6.66 - 8.33: 7 Bond angle restraints: 12367 Sorted by residual: angle pdb=" N ASP B 177 " pdb=" CA ASP B 177 " pdb=" C ASP B 177 " ideal model delta sigma weight residual 110.80 119.08 -8.28 2.13e+00 2.20e-01 1.51e+01 angle pdb=" N LYS A 431 " pdb=" CA LYS A 431 " pdb=" C LYS A 431 " ideal model delta sigma weight residual 112.92 108.63 4.29 1.23e+00 6.61e-01 1.21e+01 angle pdb=" CA GLU B 42 " pdb=" CB GLU B 42 " pdb=" CG GLU B 42 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CA THR A 240 " pdb=" CB THR A 240 " pdb=" CG2 THR A 240 " ideal model delta sigma weight residual 110.50 116.09 -5.59 1.70e+00 3.46e-01 1.08e+01 angle pdb=" N ASP A 256 " pdb=" CA ASP A 256 " pdb=" CB ASP A 256 " ideal model delta sigma weight residual 110.16 105.33 4.83 1.48e+00 4.57e-01 1.07e+01 ... (remaining 12362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4666 17.43 - 34.87: 445 34.87 - 52.30: 128 52.30 - 69.73: 86 69.73 - 87.16: 32 Dihedral angle restraints: 5357 sinusoidal: 2570 harmonic: 2787 Sorted by residual: dihedral pdb=" CA ASN B 418 " pdb=" C ASN B 418 " pdb=" N THR B 419 " pdb=" CA THR B 419 " ideal model delta harmonic sigma weight residual 180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA GLU A 194 " pdb=" C GLU A 194 " pdb=" N ILE A 195 " pdb=" CA ILE A 195 " ideal model delta harmonic sigma weight residual -180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA GLY A 490 " pdb=" C GLY A 490 " pdb=" N LEU A 491 " pdb=" CA LEU A 491 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 5354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1257 0.077 - 0.153: 143 0.153 - 0.230: 17 0.230 - 0.307: 16 0.307 - 0.383: 4 Chirality restraints: 1437 Sorted by residual: chirality pdb=" CG LEU A 491 " pdb=" CB LEU A 491 " pdb=" CD1 LEU A 491 " pdb=" CD2 LEU A 491 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB VAL B 261 " pdb=" CA VAL B 261 " pdb=" CG1 VAL B 261 " pdb=" CG2 VAL B 261 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB VAL A 423 " pdb=" CA VAL A 423 " pdb=" CG1 VAL A 423 " pdb=" CG2 VAL A 423 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 1434 not shown) Planarity restraints: 1358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 194 " 0.014 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" CD GLU A 194 " -0.050 2.00e-02 2.50e+03 pdb=" OE1 GLU A 194 " 0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU A 194 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 300 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C GLU A 300 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU A 300 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 301 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 370 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" CD GLU A 370 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 370 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 370 " -0.013 2.00e-02 2.50e+03 ... (remaining 1355 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 51 2.52 - 3.12: 6402 3.12 - 3.71: 13680 3.71 - 4.31: 17409 4.31 - 4.90: 27770 Nonbonded interactions: 65312 Sorted by model distance: nonbonded pdb=" O ASP B 177 " pdb=" OD1 ASP B 177 " model vdw 1.931 3.040 nonbonded pdb=" O THR A 215 " pdb=" OG1 THR A 216 " model vdw 2.127 3.040 nonbonded pdb=" O PHE A 61 " pdb=" CD2 LEU A 74 " model vdw 2.207 3.460 nonbonded pdb=" OG SER B 379 " pdb=" O LYS B 385 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU A 492 " pdb=" OE2 GLU A 529 " model vdw 2.237 3.040 ... (remaining 65307 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: 0.770 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.470 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.004 0.070 8873 Z= 0.260 Angle : 0.788 8.330 12367 Z= 0.423 Chirality : 0.058 0.383 1437 Planarity : 0.005 0.050 1358 Dihedral : 17.883 87.163 3559 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.27 % Allowed : 5.08 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -4.73 (0.22), residues: 945 helix: -2.19 (0.23), residues: 310 sheet: -3.76 (0.43), residues: 93 loop : -3.78 (0.22), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 402 HIS 0.005 0.001 HIS B 198 PHE 0.017 0.002 PHE B 416 TYR 0.013 0.001 TYR B 339 ARG 0.002 0.000 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.7908 (t80) cc_final: 0.7656 (t80) REVERT: A 181 TYR cc_start: 0.7804 (m-10) cc_final: 0.6386 (m-10) REVERT: A 246 LEU cc_start: 0.8617 (tp) cc_final: 0.8357 (tp) REVERT: A 373 GLN cc_start: 0.8584 (pp30) cc_final: 0.8256 (tm-30) REVERT: A 524 GLN cc_start: 0.8040 (tt0) cc_final: 0.7661 (tt0) REVERT: A 552 VAL cc_start: 0.9119 (m) cc_final: 0.8882 (t) REVERT: B 75 VAL cc_start: 0.8919 (t) cc_final: 0.8694 (t) REVERT: B 254 VAL cc_start: 0.8808 (t) cc_final: 0.7895 (t) REVERT: B 258 GLN cc_start: 0.8897 (mt0) cc_final: 0.8690 (mp10) REVERT: B 318 TYR cc_start: 0.7723 (m-80) cc_final: 0.7132 (m-80) REVERT: B 395 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8177 (ttpt) REVERT: B 405 TYR cc_start: 0.7679 (m-80) cc_final: 0.7172 (m-80) outliers start: 2 outliers final: 0 residues processed: 179 average time/residue: 0.2683 time to fit residues: 61.6674 Evaluate side-chains 95 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.0270 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 315 HIS A 394 GLN A 475 GLN A 507 GLN A 524 GLN A 547 GLN B 145 GLN B 332 GLN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.098829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082271 restraints weight = 24975.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.084035 restraints weight = 14025.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.085230 restraints weight = 9224.404| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8873 Z= 0.172 Angle : 0.605 7.439 12367 Z= 0.300 Chirality : 0.042 0.143 1437 Planarity : 0.005 0.051 1358 Dihedral : 16.785 74.202 1845 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.27 % Allowed : 4.41 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.27 (0.25), residues: 945 helix: -0.47 (0.29), residues: 313 sheet: -3.24 (0.44), residues: 101 loop : -3.17 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 402 HIS 0.004 0.001 HIS A 221 PHE 0.018 0.001 PHE A 171 TYR 0.012 0.001 TYR A 457 ARG 0.006 0.001 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.7968 (t80) cc_final: 0.7739 (t80) REVERT: A 246 LEU cc_start: 0.8312 (tp) cc_final: 0.7990 (tt) REVERT: A 351 THR cc_start: 0.9359 (t) cc_final: 0.9031 (p) REVERT: A 524 GLN cc_start: 0.8324 (tt0) cc_final: 0.7913 (tt0) REVERT: A 552 VAL cc_start: 0.9047 (m) cc_final: 0.8773 (p) REVERT: B 75 VAL cc_start: 0.8989 (t) cc_final: 0.8676 (t) REVERT: B 254 VAL cc_start: 0.8877 (t) cc_final: 0.7949 (t) REVERT: B 318 TYR cc_start: 0.7788 (m-80) cc_final: 0.7189 (m-80) REVERT: B 395 LYS cc_start: 0.8662 (ttpp) cc_final: 0.8438 (tptt) outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.2093 time to fit residues: 40.5604 Evaluate side-chains 89 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 0.0470 chunk 75 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 507 GLN B 151 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.096579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.079393 restraints weight = 25195.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.081324 restraints weight = 13465.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.082596 restraints weight = 8560.529| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8873 Z= 0.188 Angle : 0.574 6.763 12367 Z= 0.282 Chirality : 0.041 0.140 1437 Planarity : 0.004 0.052 1358 Dihedral : 16.664 74.116 1845 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.76 (0.26), residues: 945 helix: 0.10 (0.29), residues: 316 sheet: -3.35 (0.39), residues: 128 loop : -2.79 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 402 HIS 0.003 0.001 HIS A 221 PHE 0.014 0.002 PHE B 416 TYR 0.009 0.001 TYR A 457 ARG 0.003 0.001 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8347 (mmp) cc_final: 0.8045 (mmm) REVERT: A 181 TYR cc_start: 0.8022 (m-10) cc_final: 0.6537 (m-10) REVERT: A 210 LEU cc_start: 0.8604 (tp) cc_final: 0.8198 (pp) REVERT: A 246 LEU cc_start: 0.8458 (tp) cc_final: 0.8019 (tt) REVERT: A 370 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 524 GLN cc_start: 0.8455 (tt0) cc_final: 0.7999 (tt0) REVERT: A 552 VAL cc_start: 0.9103 (m) cc_final: 0.8849 (p) REVERT: B 75 VAL cc_start: 0.9140 (t) cc_final: 0.8882 (t) REVERT: B 254 VAL cc_start: 0.8746 (t) cc_final: 0.8097 (t) REVERT: B 258 GLN cc_start: 0.8987 (mt0) cc_final: 0.8731 (mp10) REVERT: B 318 TYR cc_start: 0.7882 (m-80) cc_final: 0.7196 (m-80) REVERT: B 395 LYS cc_start: 0.8832 (ttpp) cc_final: 0.8590 (tptp) outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.2030 time to fit residues: 35.5753 Evaluate side-chains 82 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 41 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 0.0770 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN B 147 ASN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.095377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077826 restraints weight = 25020.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.079694 restraints weight = 13692.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.080949 restraints weight = 8878.756| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8873 Z= 0.201 Angle : 0.568 6.813 12367 Z= 0.278 Chirality : 0.040 0.131 1437 Planarity : 0.004 0.054 1358 Dihedral : 16.605 74.116 1845 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.40 (0.27), residues: 945 helix: 0.32 (0.29), residues: 325 sheet: -3.00 (0.41), residues: 128 loop : -2.61 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 402 HIS 0.003 0.001 HIS B 198 PHE 0.015 0.002 PHE A 171 TYR 0.016 0.001 TYR A 339 ARG 0.006 0.001 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8415 (mmp) cc_final: 0.8076 (mmm) REVERT: A 210 LEU cc_start: 0.8619 (tp) cc_final: 0.8139 (pp) REVERT: A 246 LEU cc_start: 0.8608 (tp) cc_final: 0.8160 (tt) REVERT: A 370 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8170 (tp30) REVERT: A 524 GLN cc_start: 0.8427 (tt0) cc_final: 0.7929 (tt0) REVERT: A 552 VAL cc_start: 0.9100 (m) cc_final: 0.8854 (p) REVERT: B 318 TYR cc_start: 0.7930 (m-80) cc_final: 0.7286 (m-80) REVERT: B 426 TRP cc_start: 0.7294 (t60) cc_final: 0.7039 (t60) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2265 time to fit residues: 38.2394 Evaluate side-chains 80 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.078055 restraints weight = 24741.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.079919 restraints weight = 13593.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.081203 restraints weight = 8874.070| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8873 Z= 0.164 Angle : 0.548 6.994 12367 Z= 0.269 Chirality : 0.040 0.142 1437 Planarity : 0.004 0.055 1358 Dihedral : 16.546 74.136 1845 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.03 (0.27), residues: 945 helix: 0.57 (0.30), residues: 325 sheet: -2.73 (0.42), residues: 137 loop : -2.33 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 402 HIS 0.003 0.001 HIS B 198 PHE 0.017 0.002 PHE A 171 TYR 0.024 0.001 TYR A 405 ARG 0.006 0.001 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.8041 (m-10) cc_final: 0.6579 (m-10) REVERT: A 210 LEU cc_start: 0.8553 (tp) cc_final: 0.8078 (pp) REVERT: A 246 LEU cc_start: 0.8420 (tp) cc_final: 0.8036 (tt) REVERT: A 370 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8103 (tp30) REVERT: A 524 GLN cc_start: 0.8340 (tt0) cc_final: 0.8068 (tt0) REVERT: A 552 VAL cc_start: 0.9106 (m) cc_final: 0.8874 (p) REVERT: B 279 LEU cc_start: 0.9012 (mp) cc_final: 0.8671 (mt) REVERT: B 318 TYR cc_start: 0.7920 (m-80) cc_final: 0.7312 (m-80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2046 time to fit residues: 33.3811 Evaluate side-chains 82 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.0270 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.093949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.076252 restraints weight = 25151.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.078083 restraints weight = 13768.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.079308 restraints weight = 8971.164| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8873 Z= 0.197 Angle : 0.566 7.086 12367 Z= 0.276 Chirality : 0.039 0.137 1437 Planarity : 0.004 0.056 1358 Dihedral : 16.538 74.124 1845 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.28), residues: 945 helix: 0.69 (0.30), residues: 328 sheet: -2.58 (0.42), residues: 137 loop : -2.18 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 88 HIS 0.003 0.001 HIS B 198 PHE 0.020 0.002 PHE A 171 TYR 0.017 0.001 TYR A 405 ARG 0.005 0.001 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.6975 (t0) cc_final: 0.6668 (t70) REVERT: A 370 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8124 (tp30) REVERT: A 439 THR cc_start: 0.9522 (p) cc_final: 0.9180 (t) REVERT: A 552 VAL cc_start: 0.9125 (m) cc_final: 0.8914 (p) REVERT: B 34 LEU cc_start: 0.8523 (mt) cc_final: 0.8220 (mt) REVERT: B 178 ILE cc_start: 0.9335 (mt) cc_final: 0.9099 (tt) REVERT: B 279 LEU cc_start: 0.9038 (mp) cc_final: 0.8751 (mt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2071 time to fit residues: 31.4904 Evaluate side-chains 76 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076019 restraints weight = 25232.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077883 restraints weight = 13612.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.079145 restraints weight = 8795.721| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8873 Z= 0.190 Angle : 0.564 6.677 12367 Z= 0.275 Chirality : 0.040 0.153 1437 Planarity : 0.004 0.056 1358 Dihedral : 16.524 74.140 1845 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.28), residues: 945 helix: 0.85 (0.30), residues: 325 sheet: -2.37 (0.43), residues: 138 loop : -1.99 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 414 HIS 0.002 0.001 HIS B 198 PHE 0.022 0.002 PHE A 171 TYR 0.016 0.001 TYR A 405 ARG 0.006 0.001 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 181 TYR cc_start: 0.8886 (m-10) cc_final: 0.8450 (m-10) REVERT: A 370 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8270 (tp30) REVERT: A 439 THR cc_start: 0.9533 (p) cc_final: 0.9258 (t) REVERT: A 491 LEU cc_start: 0.8561 (tt) cc_final: 0.8353 (tt) REVERT: A 552 VAL cc_start: 0.9151 (m) cc_final: 0.8946 (p) REVERT: B 279 LEU cc_start: 0.9049 (mp) cc_final: 0.8837 (mt) REVERT: B 307 ARG cc_start: 0.8326 (mpp80) cc_final: 0.7866 (mtm-85) REVERT: B 378 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7638 (tt0) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2517 time to fit residues: 35.8576 Evaluate side-chains 76 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.076465 restraints weight = 25380.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.078340 restraints weight = 13640.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.079610 restraints weight = 8782.402| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8873 Z= 0.166 Angle : 0.549 7.815 12367 Z= 0.267 Chirality : 0.040 0.168 1437 Planarity : 0.004 0.057 1358 Dihedral : 16.505 74.157 1845 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.28), residues: 945 helix: 0.95 (0.30), residues: 325 sheet: -2.29 (0.43), residues: 138 loop : -1.91 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 414 HIS 0.002 0.000 HIS B 96 PHE 0.023 0.002 PHE A 171 TYR 0.013 0.001 TYR A 405 ARG 0.004 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8487 (tp) cc_final: 0.7933 (pp) REVERT: A 370 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8279 (tp30) REVERT: B 34 LEU cc_start: 0.8709 (mt) cc_final: 0.8185 (mm) REVERT: B 279 LEU cc_start: 0.8972 (mp) cc_final: 0.8758 (mt) REVERT: B 307 ARG cc_start: 0.8405 (mpp80) cc_final: 0.8018 (mtm-85) REVERT: B 395 LYS cc_start: 0.9119 (tmtt) cc_final: 0.8776 (ttpt) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2423 time to fit residues: 33.7753 Evaluate side-chains 77 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.094652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076752 restraints weight = 25613.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.078660 restraints weight = 13596.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.079965 restraints weight = 8749.725| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8873 Z= 0.161 Angle : 0.557 7.408 12367 Z= 0.271 Chirality : 0.040 0.157 1437 Planarity : 0.004 0.059 1358 Dihedral : 16.499 74.161 1845 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.28), residues: 945 helix: 0.88 (0.30), residues: 331 sheet: -1.91 (0.46), residues: 128 loop : -1.98 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 212 HIS 0.005 0.001 HIS A 221 PHE 0.024 0.002 PHE A 171 TYR 0.013 0.001 TYR A 405 ARG 0.004 0.001 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8301 (tp30) REVERT: B 307 ARG cc_start: 0.8443 (mpp80) cc_final: 0.8023 (mtm-85) REVERT: B 395 LYS cc_start: 0.9135 (tmtt) cc_final: 0.8727 (ttpt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2264 time to fit residues: 30.0528 Evaluate side-chains 78 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 80 optimal weight: 0.1980 chunk 82 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN B 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077999 restraints weight = 25463.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.079940 restraints weight = 13611.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081235 restraints weight = 8750.631| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8873 Z= 0.141 Angle : 0.552 7.046 12367 Z= 0.266 Chirality : 0.040 0.164 1437 Planarity : 0.004 0.052 1358 Dihedral : 16.474 74.159 1845 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.28), residues: 945 helix: 0.96 (0.30), residues: 331 sheet: -1.89 (0.45), residues: 133 loop : -1.84 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 402 HIS 0.002 0.001 HIS B 96 PHE 0.025 0.002 PHE A 171 TYR 0.011 0.001 TYR A 405 ARG 0.008 0.001 ARG A 358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8257 (tp30) REVERT: A 491 LEU cc_start: 0.8631 (tt) cc_final: 0.8040 (tt) REVERT: B 307 ARG cc_start: 0.8475 (mpp80) cc_final: 0.8139 (mtm-85) REVERT: B 395 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8684 (ttpt) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.2151 time to fit residues: 31.0399 Evaluate side-chains 83 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 96 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 255 ASN B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.094934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076961 restraints weight = 25684.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078891 restraints weight = 13800.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.080192 restraints weight = 8895.258| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8873 Z= 0.159 Angle : 0.552 7.021 12367 Z= 0.269 Chirality : 0.040 0.165 1437 Planarity : 0.004 0.051 1358 Dihedral : 16.486 74.145 1845 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.28), residues: 945 helix: 0.86 (0.30), residues: 332 sheet: -1.84 (0.45), residues: 133 loop : -1.80 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 414 HIS 0.003 0.001 HIS A 96 PHE 0.012 0.001 PHE B 416 TYR 0.012 0.001 TYR A 405 ARG 0.006 0.001 ARG A 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2499.80 seconds wall clock time: 45 minutes 22.71 seconds (2722.71 seconds total)