Starting phenix.real_space_refine on Sat Dec 28 17:07:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6waz_21582/12_2024/6waz_21582.cif Found real_map, /net/cci-nas-00/data/ceres_data/6waz_21582/12_2024/6waz_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_21582/12_2024/6waz_21582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6waz_21582/12_2024/6waz_21582.map" model { file = "/net/cci-nas-00/data/ceres_data/6waz_21582/12_2024/6waz_21582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6waz_21582/12_2024/6waz_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-5532/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: 5.92, per 1000 atoms: 0.69 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: 2.63 Conformation dependent library (CDL) restraints added in 922.8 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: 2.79 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: 2.94 Time building geometry restraints manager: 2.95 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: 3.010 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: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 25.160 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- 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 : 0.921 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: 0.2742 time to fit residues: 62.9637 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 : 1.019 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2113 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= 0.173 Angle : 0.605 7.435 12367 Z= 0.300 Chirality : 0.042 0.143 1437 Planarity : 0.005 0.051 1358 Dihedral : 16.785 74.203 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: -0.46 (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 : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.7903 (t80) cc_final: 0.7683 (t80) REVERT: A 246 LEU cc_start: 0.8302 (tp) cc_final: 0.7981 (tt) REVERT: A 351 THR cc_start: 0.9353 (t) cc_final: 0.9023 (p) REVERT: A 524 GLN cc_start: 0.8264 (tt0) cc_final: 0.7856 (tt0) REVERT: A 552 VAL cc_start: 0.9055 (m) cc_final: 0.8781 (p) REVERT: B 75 VAL cc_start: 0.9009 (t) cc_final: 0.8701 (t) REVERT: B 254 VAL cc_start: 0.8876 (t) cc_final: 0.7945 (t) REVERT: B 318 TYR cc_start: 0.7736 (m-80) cc_final: 0.7152 (m-80) REVERT: B 395 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8432 (tptt) outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.2237 time to fit residues: 43.3029 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 : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.6182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8873 Z= 0.250 Angle : 0.610 6.311 12367 Z= 0.302 Chirality : 0.042 0.145 1437 Planarity : 0.004 0.052 1358 Dihedral : 16.717 74.233 1845 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.13 % Allowed : 4.41 % Favored : 95.45 % 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: -2.88 (0.26), residues: 945 helix: -0.03 (0.29), residues: 317 sheet: -3.40 (0.38), residues: 128 loop : -2.86 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 426 HIS 0.003 0.001 HIS B 198 PHE 0.014 0.002 PHE B 416 TYR 0.012 0.001 TYR A 441 ARG 0.003 0.001 ARG A 284 *********************** 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 125 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8325 (mmp) cc_final: 0.8029 (mmm) REVERT: A 145 GLN cc_start: 0.7860 (pm20) cc_final: 0.7519 (pt0) REVERT: A 181 TYR cc_start: 0.7895 (m-10) cc_final: 0.6517 (m-10) REVERT: A 210 LEU cc_start: 0.8589 (tp) cc_final: 0.8175 (pp) REVERT: A 246 LEU cc_start: 0.8498 (tp) cc_final: 0.8087 (tt) REVERT: A 370 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8416 (mm-30) REVERT: A 483 TYR cc_start: 0.8701 (t80) cc_final: 0.8199 (t80) REVERT: A 524 GLN cc_start: 0.8220 (tt0) cc_final: 0.7894 (tt0) REVERT: A 552 VAL cc_start: 0.9126 (m) cc_final: 0.8890 (p) REVERT: B 75 VAL cc_start: 0.9193 (t) cc_final: 0.8971 (t) REVERT: B 254 VAL cc_start: 0.8752 (t) cc_final: 0.8094 (t) REVERT: B 258 GLN cc_start: 0.8997 (mt0) cc_final: 0.8752 (mp10) REVERT: B 318 TYR cc_start: 0.7838 (m-80) cc_final: 0.7146 (m-80) REVERT: B 378 GLU cc_start: 0.8221 (mt-10) cc_final: 0.8004 (tt0) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.2243 time to fit residues: 38.6059 Evaluate side-chains 79 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.2980 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 147 ASN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8873 Z= 0.154 Angle : 0.554 7.701 12367 Z= 0.270 Chirality : 0.040 0.130 1437 Planarity : 0.004 0.054 1358 Dihedral : 16.586 74.138 1845 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -2.31 (0.27), residues: 945 helix: 0.39 (0.30), residues: 324 sheet: -2.94 (0.42), residues: 129 loop : -2.54 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 402 HIS 0.003 0.001 HIS A 221 PHE 0.014 0.001 PHE A 171 TYR 0.015 0.001 TYR A 339 ARG 0.005 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 127 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8352 (mmp) cc_final: 0.8121 (mmm) REVERT: A 210 LEU cc_start: 0.8445 (tp) cc_final: 0.8065 (pp) REVERT: A 246 LEU cc_start: 0.8531 (tp) cc_final: 0.8110 (tt) REVERT: A 370 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8236 (mm-30) REVERT: A 524 GLN cc_start: 0.8233 (tt0) cc_final: 0.7767 (tt0) REVERT: A 552 VAL cc_start: 0.9087 (m) cc_final: 0.8839 (p) REVERT: B 279 LEU cc_start: 0.8918 (mp) cc_final: 0.8659 (mt) REVERT: B 318 TYR cc_start: 0.7796 (m-80) cc_final: 0.7176 (m-80) REVERT: B 378 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7952 (tt0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1907 time to fit residues: 34.7451 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 : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0040 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 0.0570 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 overall best weight: 1.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8873 Z= 0.234 Angle : 0.591 6.387 12367 Z= 0.292 Chirality : 0.040 0.133 1437 Planarity : 0.004 0.054 1358 Dihedral : 16.601 74.143 1845 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -2.10 (0.27), residues: 945 helix: 0.57 (0.30), residues: 328 sheet: -2.79 (0.42), residues: 128 loop : -2.47 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 414 HIS 0.003 0.001 HIS B 198 PHE 0.018 0.002 PHE A 171 TYR 0.024 0.002 TYR A 405 ARG 0.006 0.001 ARG A 211 *********************** 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 109 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.8145 (m-10) cc_final: 0.7371 (m-10) REVERT: A 210 LEU cc_start: 0.8497 (tp) cc_final: 0.8086 (pp) REVERT: A 246 LEU cc_start: 0.8459 (tp) cc_final: 0.8096 (tt) REVERT: A 370 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8204 (tp30) REVERT: A 524 GLN cc_start: 0.8146 (tt0) cc_final: 0.7860 (tt0) REVERT: A 552 VAL cc_start: 0.9100 (m) cc_final: 0.8895 (p) REVERT: B 212 TRP cc_start: 0.6467 (t60) cc_final: 0.5837 (m100) REVERT: B 279 LEU cc_start: 0.8901 (mp) cc_final: 0.8653 (mt) REVERT: B 318 TYR cc_start: 0.7888 (m-80) cc_final: 0.7272 (m-80) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2182 time to fit residues: 33.4362 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 : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8873 Z= 0.227 Angle : 0.577 6.341 12367 Z= 0.285 Chirality : 0.041 0.146 1437 Planarity : 0.004 0.056 1358 Dihedral : 16.585 74.151 1845 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -1.83 (0.27), residues: 945 helix: 0.64 (0.30), residues: 330 sheet: -2.32 (0.46), residues: 118 loop : -2.31 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 414 HIS 0.003 0.001 HIS B 198 PHE 0.021 0.002 PHE A 171 TYR 0.015 0.001 TYR A 405 ARG 0.003 0.000 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 111 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.8321 (m-10) cc_final: 0.7546 (m-10) REVERT: A 246 LEU cc_start: 0.8612 (tp) cc_final: 0.8265 (tt) REVERT: A 370 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8308 (tp30) REVERT: A 552 VAL cc_start: 0.9198 (m) cc_final: 0.8979 (p) REVERT: B 34 LEU cc_start: 0.8580 (mt) cc_final: 0.8240 (mt) REVERT: B 178 ILE cc_start: 0.9325 (mt) cc_final: 0.9103 (tt) REVERT: B 279 LEU cc_start: 0.8888 (mp) cc_final: 0.8664 (mt) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2166 time to fit residues: 34.0401 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 : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** A 306 ASN A 475 GLN B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4225 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= 0.163 Angle : 0.549 6.396 12367 Z= 0.268 Chirality : 0.039 0.133 1437 Planarity : 0.004 0.057 1358 Dihedral : 16.537 74.185 1845 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % 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: -1.52 (0.28), residues: 945 helix: 0.92 (0.31), residues: 330 sheet: -2.19 (0.45), residues: 128 loop : -2.11 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 414 HIS 0.002 0.001 HIS B 198 PHE 0.022 0.002 PHE A 171 TYR 0.015 0.001 TYR A 405 ARG 0.003 0.000 ARG A 211 *********************** 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 107 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8088 (tp) cc_final: 0.7862 (tt) REVERT: A 181 TYR cc_start: 0.8357 (m-10) cc_final: 0.7471 (m-10) REVERT: A 370 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8265 (tp30) REVERT: A 552 VAL cc_start: 0.9194 (m) cc_final: 0.8975 (p) REVERT: B 279 LEU cc_start: 0.8860 (mp) cc_final: 0.8634 (mt) REVERT: B 307 ARG cc_start: 0.8357 (mpp80) cc_final: 0.7934 (mtm-85) REVERT: B 395 LYS cc_start: 0.9209 (tptp) cc_final: 0.8850 (ttpt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2200 time to fit residues: 32.3792 Evaluate side-chains 75 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.0070 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.9604 ------------------------------------------------------------------------------- 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 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8873 Z= 0.177 Angle : 0.550 6.550 12367 Z= 0.269 Chirality : 0.040 0.132 1437 Planarity : 0.004 0.058 1358 Dihedral : 16.536 74.179 1845 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % 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: -1.50 (0.28), residues: 945 helix: 0.91 (0.30), residues: 335 sheet: -1.94 (0.47), residues: 118 loop : -2.20 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 414 HIS 0.002 0.001 HIS B 208 PHE 0.023 0.002 PHE A 171 TYR 0.013 0.001 TYR A 405 ARG 0.004 0.000 ARG B 125 *********************** 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 102 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 181 TYR cc_start: 0.8387 (m-10) cc_final: 0.7466 (m-10) REVERT: A 246 LEU cc_start: 0.8544 (tp) cc_final: 0.8329 (tt) REVERT: A 340 GLN cc_start: 0.7422 (mp10) cc_final: 0.7217 (mt0) REVERT: A 370 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8276 (tp30) REVERT: A 552 VAL cc_start: 0.9166 (m) cc_final: 0.8922 (p) REVERT: B 34 LEU cc_start: 0.8773 (mt) cc_final: 0.8271 (mm) REVERT: B 279 LEU cc_start: 0.8906 (mp) cc_final: 0.8692 (mt) REVERT: B 307 ARG cc_start: 0.8373 (mpp80) cc_final: 0.8017 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2253 time to fit residues: 32.7220 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 : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.0050 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 255 ASN B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8873 Z= 0.158 Angle : 0.555 7.403 12367 Z= 0.269 Chirality : 0.039 0.129 1437 Planarity : 0.004 0.050 1358 Dihedral : 16.508 74.194 1845 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -1.36 (0.28), residues: 945 helix: 0.96 (0.31), residues: 335 sheet: -1.94 (0.45), residues: 128 loop : -2.02 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 414 HIS 0.003 0.001 HIS B 198 PHE 0.022 0.002 PHE A 171 TYR 0.012 0.001 TYR A 405 ARG 0.003 0.000 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 102 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 181 TYR cc_start: 0.8351 (m-10) cc_final: 0.7413 (m-10) REVERT: A 370 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8255 (tp30) REVERT: B 212 TRP cc_start: 0.6640 (t60) cc_final: 0.6098 (m-90) REVERT: B 279 LEU cc_start: 0.8850 (mp) cc_final: 0.8621 (mt) REVERT: B 307 ARG cc_start: 0.8392 (mpp80) cc_final: 0.8093 (mtm-85) REVERT: B 395 LYS cc_start: 0.9255 (tptp) cc_final: 0.8886 (ttpt) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2253 time to fit residues: 31.7184 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 : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0170 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8873 Z= 0.174 Angle : 0.560 8.319 12367 Z= 0.271 Chirality : 0.040 0.140 1437 Planarity : 0.004 0.051 1358 Dihedral : 16.515 74.188 1845 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -1.27 (0.28), residues: 945 helix: 0.89 (0.30), residues: 337 sheet: -1.80 (0.47), residues: 116 loop : -1.90 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 414 HIS 0.002 0.001 HIS B 198 PHE 0.021 0.002 PHE A 171 TYR 0.012 0.001 TYR A 405 ARG 0.004 0.000 ARG A 211 ********************** 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 99 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 370 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8378 (tp30) REVERT: B 279 LEU cc_start: 0.8866 (mp) cc_final: 0.8641 (mt) REVERT: B 307 ARG cc_start: 0.8405 (mpp80) cc_final: 0.8127 (mtm-85) REVERT: B 395 LYS cc_start: 0.9298 (tptp) cc_final: 0.8905 (ttpt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2070 time to fit residues: 29.0400 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 : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** A 519 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 = 0.3403 r_free = 0.3403 target = 0.093213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075027 restraints weight = 25825.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076928 restraints weight = 13876.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.078198 restraints weight = 9010.962| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8873 Z= 0.167 Angle : 0.555 7.785 12367 Z= 0.267 Chirality : 0.040 0.144 1437 Planarity : 0.004 0.048 1358 Dihedral : 16.515 74.194 1845 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: -1.22 (0.28), residues: 945 helix: 0.91 (0.30), residues: 337 sheet: -1.76 (0.46), residues: 119 loop : -1.86 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 414 HIS 0.002 0.001 HIS B 198 PHE 0.020 0.002 PHE A 171 TYR 0.012 0.001 TYR A 405 ARG 0.003 0.000 ARG A 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1779.63 seconds wall clock time: 33 minutes 37.17 seconds (2017.17 seconds total)