Starting phenix.real_space_refine on Thu Feb 13 08:44:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6waz_21582/02_2025/6waz_21582.cif Found real_map, /net/cci-nas-00/data/ceres_data/6waz_21582/02_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_21582/02_2025/6waz_21582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6waz_21582/02_2025/6waz_21582.map" model { file = "/net/cci-nas-00/data/ceres_data/6waz_21582/02_2025/6waz_21582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6waz_21582/02_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-5592/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: 5.38, per 1000 atoms: 0.63 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: 2.56 Conformation dependent library (CDL) restraints added in 860.5 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: 2.88 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: 2.65 Time building geometry restraints manager: 2.90 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: 0.010 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- 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 : 0.849 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: 0.2836 time to fit residues: 64.8958 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 : 0.961 ------------------------------------------------------------------------------- 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 = 0.098827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082269 restraints weight = 24976.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.084030 restraints weight = 14023.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085209 restraints weight = 9236.869| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.7969 (t80) cc_final: 0.7738 (t80) REVERT: A 246 LEU cc_start: 0.8311 (tp) cc_final: 0.7990 (tt) REVERT: A 351 THR cc_start: 0.9361 (t) cc_final: 0.9031 (p) REVERT: A 524 GLN cc_start: 0.8306 (tt0) cc_final: 0.7895 (tt0) REVERT: A 552 VAL cc_start: 0.9048 (m) cc_final: 0.8773 (p) REVERT: B 75 VAL cc_start: 0.8990 (t) cc_final: 0.8678 (t) REVERT: B 254 VAL cc_start: 0.8878 (t) cc_final: 0.7950 (t) REVERT: B 318 TYR cc_start: 0.7788 (m-80) cc_final: 0.7188 (m-80) REVERT: B 395 LYS cc_start: 0.8663 (ttpp) cc_final: 0.8439 (tptt) outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.2200 time to fit residues: 42.6734 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 : 0.933 ------------------------------------------------------------------------------- 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: 2.9990 chunk 89 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.077726 restraints weight = 25234.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.079577 restraints weight = 13594.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.080844 restraints weight = 8766.485| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8873 Z= 0.242 Angle : 0.605 6.769 12367 Z= 0.299 Chirality : 0.041 0.145 1437 Planarity : 0.004 0.051 1358 Dihedral : 16.699 74.201 1845 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.13 % Allowed : 4.28 % Favored : 95.59 % 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: -2.89 (0.26), residues: 945 helix: -0.06 (0.29), residues: 323 sheet: -3.35 (0.39), residues: 128 loop : -2.90 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 426 HIS 0.003 0.001 HIS B 198 PHE 0.014 0.002 PHE B 416 TYR 0.011 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 : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8354 (mmp) cc_final: 0.8055 (mmm) REVERT: A 181 TYR cc_start: 0.8018 (m-10) cc_final: 0.6593 (m-10) REVERT: A 210 LEU cc_start: 0.8669 (tp) cc_final: 0.8224 (pp) REVERT: A 246 LEU cc_start: 0.8507 (tp) cc_final: 0.7984 (tt) REVERT: A 370 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8341 (mm-30) REVERT: A 483 TYR cc_start: 0.8708 (t80) cc_final: 0.8245 (t80) REVERT: A 524 GLN cc_start: 0.8327 (tt0) cc_final: 0.7870 (tt0) REVERT: A 552 VAL cc_start: 0.9124 (m) cc_final: 0.8880 (p) REVERT: B 75 VAL cc_start: 0.9183 (t) cc_final: 0.8946 (t) REVERT: B 254 VAL cc_start: 0.8753 (t) cc_final: 0.8172 (t) REVERT: B 258 GLN cc_start: 0.8984 (mt0) cc_final: 0.8702 (mp10) REVERT: B 318 TYR cc_start: 0.7900 (m-80) cc_final: 0.7192 (m-80) REVERT: B 378 GLU cc_start: 0.8225 (mt-10) cc_final: 0.8001 (tt0) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.2186 time to fit residues: 37.7376 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 : 0.883 ------------------------------------------------------------------------------- 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: 1.9990 chunk 88 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 0.0070 chunk 10 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 41 optimal weight: 0.0570 chunk 15 optimal weight: 0.4980 chunk 68 optimal weight: 10.0000 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.079718 restraints weight = 25064.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.081642 restraints weight = 13591.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082920 restraints weight = 8752.474| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 0.053 8873 Z= 0.147 Angle : 0.552 7.781 12367 Z= 0.268 Chirality : 0.040 0.134 1437 Planarity : 0.004 0.054 1358 Dihedral : 16.570 74.130 1845 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: -2.26 (0.27), residues: 945 helix: 0.43 (0.30), residues: 324 sheet: -2.84 (0.42), residues: 127 loop : -2.55 (0.26), residues: 494 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 0.013 0.001 TYR A 339 ARG 0.004 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 128 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8406 (mmp) cc_final: 0.8113 (mmm) REVERT: A 210 LEU cc_start: 0.8554 (tp) cc_final: 0.8130 (pp) REVERT: A 246 LEU cc_start: 0.8342 (tp) cc_final: 0.8087 (tt) REVERT: A 370 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8111 (tp30) REVERT: A 524 GLN cc_start: 0.8380 (tt0) cc_final: 0.7906 (tt0) REVERT: A 552 VAL cc_start: 0.9150 (m) cc_final: 0.8894 (p) REVERT: B 167 ILE cc_start: 0.8949 (mt) cc_final: 0.8526 (mt) REVERT: B 279 LEU cc_start: 0.8956 (mp) cc_final: 0.8708 (mt) REVERT: B 318 TYR cc_start: 0.7860 (m-80) cc_final: 0.7224 (m-80) REVERT: B 378 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7932 (tt0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1956 time to fit residues: 35.2169 Evaluate side-chains 86 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 0.3980 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 306 ASN B 255 ASN B 373 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.096338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.078664 restraints weight = 24646.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.080562 restraints weight = 13480.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081856 restraints weight = 8746.706| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8873 Z= 0.169 Angle : 0.554 7.608 12367 Z= 0.271 Chirality : 0.040 0.166 1437 Planarity : 0.004 0.055 1358 Dihedral : 16.542 74.109 1845 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: -1.99 (0.27), residues: 945 helix: 0.69 (0.30), residues: 325 sheet: -2.62 (0.44), residues: 128 loop : -2.44 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 212 HIS 0.003 0.001 HIS B 198 PHE 0.012 0.001 PHE B 130 TYR 0.023 0.001 TYR A 405 ARG 0.004 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 118 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.8353 (m-10) cc_final: 0.7540 (m-10) REVERT: A 246 LEU cc_start: 0.8107 (tp) cc_final: 0.7732 (tt) REVERT: A 370 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8112 (tp30) REVERT: A 472 THR cc_start: 0.8301 (p) cc_final: 0.8078 (p) REVERT: A 524 GLN cc_start: 0.8350 (tt0) cc_final: 0.7876 (tt0) REVERT: B 279 LEU cc_start: 0.8900 (mp) cc_final: 0.8678 (mt) REVERT: B 318 TYR cc_start: 0.7931 (m-80) cc_final: 0.7314 (m-80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2109 time to fit residues: 34.6565 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 : 0.898 ------------------------------------------------------------------------------- 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: 6.9990 chunk 4 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 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 = 0.3432 r_free = 0.3432 target = 0.094680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.076691 restraints weight = 25074.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078636 restraints weight = 13481.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.079956 restraints weight = 8673.449| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3866 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= 0.189 Angle : 0.551 6.318 12367 Z= 0.272 Chirality : 0.040 0.146 1437 Planarity : 0.004 0.056 1358 Dihedral : 16.524 74.121 1845 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % 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: -1.81 (0.28), residues: 945 helix: 0.70 (0.30), residues: 328 sheet: -2.57 (0.44), residues: 127 loop : -2.22 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 88 HIS 0.003 0.001 HIS B 198 PHE 0.016 0.002 PHE B 416 TYR 0.017 0.001 TYR A 405 ARG 0.003 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 119 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.8355 (m-10) cc_final: 0.7549 (m-10) REVERT: A 246 LEU cc_start: 0.8308 (tp) cc_final: 0.8014 (tt) REVERT: A 370 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8192 (tp30) REVERT: A 472 THR cc_start: 0.8373 (p) cc_final: 0.8128 (p) REVERT: A 552 VAL cc_start: 0.9139 (m) cc_final: 0.8916 (p) REVERT: B 34 LEU cc_start: 0.8483 (mt) cc_final: 0.8126 (mt) REVERT: B 178 ILE cc_start: 0.9360 (mt) cc_final: 0.9129 (tt) REVERT: B 279 LEU cc_start: 0.8994 (mp) cc_final: 0.8775 (mt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2273 time to fit residues: 36.7902 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 : 0.923 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 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 = 0.3406 r_free = 0.3406 target = 0.093277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075330 restraints weight = 25373.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.077201 restraints weight = 13736.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078469 restraints weight = 8856.553| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4132 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= 0.209 Angle : 0.564 6.484 12367 Z= 0.278 Chirality : 0.040 0.152 1437 Planarity : 0.004 0.056 1358 Dihedral : 16.546 74.122 1845 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % 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: -1.69 (0.28), residues: 945 helix: 0.69 (0.30), residues: 337 sheet: -2.26 (0.46), residues: 117 loop : -2.22 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 426 HIS 0.002 0.001 HIS B 96 PHE 0.013 0.002 PHE A 171 TYR 0.018 0.001 TYR A 405 ARG 0.004 0.001 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 106 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.8394 (m-10) cc_final: 0.7628 (m-10) REVERT: A 246 LEU cc_start: 0.8351 (tp) cc_final: 0.8127 (tt) REVERT: A 370 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8246 (tp30) REVERT: A 439 THR cc_start: 0.8900 (p) cc_final: 0.8695 (t) REVERT: A 552 VAL cc_start: 0.9198 (m) cc_final: 0.8970 (p) REVERT: A 556 ILE cc_start: 0.8635 (mm) cc_final: 0.8430 (mm) REVERT: B 279 LEU cc_start: 0.8996 (mp) cc_final: 0.8792 (mt) REVERT: B 307 ARG cc_start: 0.8406 (mpp80) cc_final: 0.7979 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2052 time to fit residues: 30.0205 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 : 0.966 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN B 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.075967 restraints weight = 25323.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077870 restraints weight = 13491.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.079130 restraints weight = 8580.442| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8873 Z= 0.169 Angle : 0.531 6.376 12367 Z= 0.260 Chirality : 0.039 0.142 1437 Planarity : 0.004 0.057 1358 Dihedral : 16.509 74.161 1845 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.13 % Allowed : 0.67 % Favored : 99.20 % 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: -1.35 (0.28), residues: 945 helix: 1.03 (0.31), residues: 328 sheet: -2.20 (0.44), residues: 127 loop : -1.94 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 414 HIS 0.004 0.001 HIS B 198 PHE 0.013 0.001 PHE B 416 TYR 0.013 0.001 TYR A 405 ARG 0.003 0.000 ARG B 199 *********************** 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 105 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.8512 (m-10) cc_final: 0.7783 (m-10) REVERT: A 246 LEU cc_start: 0.8402 (tp) cc_final: 0.8072 (tt) REVERT: A 370 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8348 (tp30) REVERT: B 34 LEU cc_start: 0.8661 (mt) cc_final: 0.8146 (mm) REVERT: B 307 ARG cc_start: 0.8443 (mpp80) cc_final: 0.8022 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.2335 time to fit residues: 33.4831 Evaluate side-chains 81 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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: 0.9990 chunk 92 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.075907 restraints weight = 25260.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077817 restraints weight = 13421.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.079099 restraints weight = 8507.423| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4514 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= 0.172 Angle : 0.547 7.030 12367 Z= 0.269 Chirality : 0.040 0.143 1437 Planarity : 0.004 0.056 1358 Dihedral : 16.513 74.170 1845 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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: -1.28 (0.28), residues: 945 helix: 1.00 (0.31), residues: 328 sheet: -2.10 (0.44), residues: 127 loop : -1.84 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 414 HIS 0.005 0.001 HIS A 221 PHE 0.031 0.002 PHE A 171 TYR 0.013 0.001 TYR A 405 ARG 0.003 0.000 ARG A 211 *********************** 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 100 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.943 Fit side-chains REVERT: A 181 TYR cc_start: 0.8501 (m-10) cc_final: 0.7826 (m-10) REVERT: A 370 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8288 (tp30) REVERT: B 177 ASP cc_start: 0.8232 (p0) cc_final: 0.8015 (p0) REVERT: B 307 ARG cc_start: 0.8468 (mpp80) cc_final: 0.8137 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2417 time to fit residues: 33.2014 Evaluate side-chains 73 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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: 0.8980 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076083 restraints weight = 25095.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077969 restraints weight = 13389.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.079236 restraints weight = 8552.279| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4650 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= 0.169 Angle : 0.549 7.558 12367 Z= 0.269 Chirality : 0.040 0.141 1437 Planarity : 0.004 0.050 1358 Dihedral : 16.513 74.178 1845 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -1.21 (0.28), residues: 945 helix: 0.96 (0.31), residues: 330 sheet: -1.96 (0.44), residues: 127 loop : -1.77 (0.28), residues: 488 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 0.031 0.002 PHE A 171 TYR 0.012 0.001 TYR A 405 ARG 0.007 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 95 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.854 Fit side-chains REVERT: A 181 TYR cc_start: 0.8570 (m-10) cc_final: 0.7891 (m-10) REVERT: A 370 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8287 (tp30) REVERT: B 177 ASP cc_start: 0.8235 (p0) cc_final: 0.8020 (p0) REVERT: B 307 ARG cc_start: 0.8459 (mpp80) cc_final: 0.8228 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2089 time to fit residues: 27.7229 Evaluate side-chains 73 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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: 0.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 0.0770 chunk 28 optimal weight: 0.0980 chunk 96 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN A 475 GLN B 197 GLN B 373 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.094856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.077161 restraints weight = 25584.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.079083 restraints weight = 13540.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.080361 restraints weight = 8651.478| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8873 Z= 0.147 Angle : 0.531 7.751 12367 Z= 0.258 Chirality : 0.039 0.140 1437 Planarity : 0.004 0.050 1358 Dihedral : 16.485 74.177 1845 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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: -1.11 (0.28), residues: 945 helix: 0.95 (0.31), residues: 329 sheet: -1.80 (0.44), residues: 127 loop : -1.65 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 402 HIS 0.003 0.001 HIS A 221 PHE 0.033 0.002 PHE A 171 TYR 0.011 0.001 TYR A 405 ARG 0.007 0.000 ARG A 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2397.12 seconds wall clock time: 44 minutes 1.00 seconds (2641.00 seconds total)