Starting phenix.real_space_refine on Fri Nov 15 10:43:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/11_2024/8phf_17660.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/11_2024/8phf_17660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/11_2024/8phf_17660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/11_2024/8phf_17660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/11_2024/8phf_17660.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/11_2024/8phf_17660.cif" } resolution = 3.6 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= 0.004 sd= 0.103 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 4 5.49 5 S 44 5.16 5 C 5488 2.51 5 N 1462 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4267 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 15, 'TRANS': 531} Chain breaks: 1 Chain: "B" Number of atoms: 4267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4267 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 15, 'TRANS': 531} Chain breaks: 1 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.64 Number of scatterers: 8640 At special positions: 0 Unit cell: (121.8, 98.28, 76.44, 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 44 16.00 P 4 15.00 O 1642 8.00 N 1462 7.00 C 5488 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 940.5 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 63.2% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.673A pdb=" N VAL A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 81 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.543A pdb=" N GLY A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.519A pdb=" N ILE A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 147 removed outlier: 3.999A pdb=" N VAL A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 3.565A pdb=" N ILE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 Proline residue: A 167 - end of helix Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.548A pdb=" N ILE A 192 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 305 through 326 removed outlier: 3.824A pdb=" N SER A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR A 325 " --> pdb=" O MET A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 368 Processing helix chain 'A' and resid 375 through 402 removed outlier: 3.762A pdb=" N ALA A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 411 through 420 removed outlier: 3.915A pdb=" N ARG A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 424 Processing helix chain 'A' and resid 431 through 449 removed outlier: 3.831A pdb=" N TYR A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 447 " --> pdb=" O HIS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 494 through 519 removed outlier: 3.594A pdb=" N ALA A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 removed outlier: 4.471A pdb=" N MET A 524 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 557 removed outlier: 3.580A pdb=" N LEU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.550A pdb=" N GLN A 585 " --> pdb=" O PHE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 609 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 60 through 81 removed outlier: 3.597A pdb=" N LEU B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) Proline residue: B 73 - end of helix Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 106 through 109 removed outlier: 3.769A pdb=" N LEU B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 106 through 109' Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.983A pdb=" N ILE B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 147 removed outlier: 3.555A pdb=" N THR B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 removed outlier: 3.546A pdb=" N ILE B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 171 Proline residue: B 167 - end of helix Processing helix chain 'B' and resid 291 through 302 removed outlier: 4.133A pdb=" N VAL B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.916A pdb=" N SER B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 329 removed outlier: 3.608A pdb=" N TYR B 325 " --> pdb=" O MET B 321 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 367 removed outlier: 4.127A pdb=" N LYS B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 401 removed outlier: 3.614A pdb=" N ALA B 379 " --> pdb=" O CYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.503A pdb=" N TYR B 406 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 407 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 removed outlier: 3.528A pdb=" N ILE B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 449 removed outlier: 3.630A pdb=" N ALA B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 447 " --> pdb=" O HIS B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 494 through 520 Processing helix chain 'B' and resid 521 through 525 removed outlier: 4.369A pdb=" N MET B 524 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 557 removed outlier: 3.690A pdb=" N LYS B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.589A pdb=" N PHE B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 585 " --> pdb=" O PHE B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 609 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 198 removed outlier: 6.489A pdb=" N TYR A 205 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 279 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU A 207 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 273 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TRP A 213 " --> pdb=" O CYS A 271 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N CYS A 271 " --> pdb=" O TRP A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 177 removed outlier: 7.464A pdb=" N ALA B 177 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE B 226 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 195 through 198 removed outlier: 6.560A pdb=" N TYR B 205 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS B 279 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU B 207 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP B 213 " --> pdb=" O CYS B 271 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N CYS B 271 " --> pdb=" O TRP B 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 330 through 331 483 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 2.72 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: 2141 1.33 - 1.45: 1616 1.45 - 1.57: 4959 1.57 - 1.69: 6 1.69 - 1.81: 70 Bond restraints: 8792 Sorted by residual: bond pdb=" O3P FAD A 701 " pdb=" P FAD A 701 " ideal model delta sigma weight residual 1.660 1.582 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" O3P FAD B 701 " pdb=" P FAD B 701 " ideal model delta sigma weight residual 1.660 1.586 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O5B FAD B 701 " pdb=" PA FAD B 701 " ideal model delta sigma weight residual 1.634 1.567 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O5B FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sigma weight residual 1.634 1.570 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O5' FAD B 701 " pdb=" P FAD B 701 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.94e+00 ... (remaining 8787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 11536 1.64 - 3.28: 271 3.28 - 4.92: 37 4.92 - 6.56: 13 6.56 - 8.20: 11 Bond angle restraints: 11868 Sorted by residual: angle pdb=" CA GLU A 426 " pdb=" CB GLU A 426 " pdb=" CG GLU A 426 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.70e+00 angle pdb=" N GLY A 186 " pdb=" CA GLY A 186 " pdb=" C GLY A 186 " ideal model delta sigma weight residual 113.18 106.51 6.67 2.37e+00 1.78e-01 7.93e+00 angle pdb=" CB MET B 124 " pdb=" CG MET B 124 " pdb=" SD MET B 124 " ideal model delta sigma weight residual 112.70 104.50 8.20 3.00e+00 1.11e-01 7.47e+00 angle pdb=" P FAD A 701 " pdb=" O3P FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sigma weight residual 130.34 122.41 7.93 3.00e+00 1.11e-01 6.99e+00 angle pdb=" CB MET B 356 " pdb=" CG MET B 356 " pdb=" SD MET B 356 " ideal model delta sigma weight residual 112.70 104.81 7.89 3.00e+00 1.11e-01 6.91e+00 ... (remaining 11863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.99: 5159 32.99 - 65.97: 150 65.97 - 98.96: 33 98.96 - 131.94: 0 131.94 - 164.93: 2 Dihedral angle restraints: 5344 sinusoidal: 2210 harmonic: 3134 Sorted by residual: dihedral pdb=" O5' FAD A 701 " pdb=" O3P FAD A 701 " pdb=" P FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sinusoidal sigma weight residual 298.23 133.30 164.93 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA PHE A 425 " pdb=" C PHE A 425 " pdb=" N GLU A 426 " pdb=" CA GLU A 426 " ideal model delta harmonic sigma weight residual 180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" O5' FAD B 701 " pdb=" O3P FAD B 701 " pdb=" P FAD B 701 " pdb=" PA FAD B 701 " ideal model delta sinusoidal sigma weight residual 298.23 163.59 134.64 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 5341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 955 0.042 - 0.084: 312 0.084 - 0.125: 67 0.125 - 0.167: 7 0.167 - 0.209: 3 Chirality restraints: 1344 Sorted by residual: chirality pdb=" C2B FAD B 701 " pdb=" C1B FAD B 701 " pdb=" C3B FAD B 701 " pdb=" O2B FAD B 701 " both_signs ideal model delta sigma weight residual False -2.53 -2.74 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ARG B 329 " pdb=" N ARG B 329 " pdb=" C ARG B 329 " pdb=" CB ARG B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PHE A 54 " pdb=" N PHE A 54 " pdb=" C PHE A 54 " pdb=" CB PHE A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 1341 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 182 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 183 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 425 " 0.009 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE A 425 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 425 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 425 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 425 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 425 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 425 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 515 " -0.008 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C LEU A 515 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 515 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 516 " -0.009 2.00e-02 2.50e+03 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 139 2.69 - 3.24: 8786 3.24 - 3.79: 13185 3.79 - 4.35: 17375 4.35 - 4.90: 28706 Nonbonded interactions: 68191 Sorted by model distance: nonbonded pdb=" O LEU A 64 " pdb=" ND2 ASN A 68 " model vdw 2.134 3.120 nonbonded pdb=" OG SER B 60 " pdb=" OE1 GLU B 63 " model vdw 2.143 3.040 nonbonded pdb=" OG SER A 60 " pdb=" OD1 ASP A 62 " model vdw 2.191 3.040 nonbonded pdb=" O3' FAD B 701 " pdb=" O5' FAD B 701 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP A 201 " pdb=" NZ LYS A 203 " model vdw 2.261 3.120 ... (remaining 68186 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.360 Find NCS groups from input model: 0.260 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 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 0.078 8792 Z= 0.286 Angle : 0.651 8.201 11868 Z= 0.327 Chirality : 0.042 0.209 1344 Planarity : 0.004 0.045 1506 Dihedral : 16.415 164.926 3332 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1086 helix: 1.03 (0.21), residues: 596 sheet: -1.02 (0.53), residues: 90 loop : 0.11 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 213 HIS 0.007 0.001 HIS A 204 PHE 0.031 0.002 PHE A 425 TYR 0.021 0.001 TYR B 361 ARG 0.006 0.000 ARG A 609 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.7705 (m-30) cc_final: 0.7184 (m-30) REVERT: A 609 ARG cc_start: 0.6539 (mmt180) cc_final: 0.6175 (tpt170) REVERT: B 619 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.7123 (ttm-80) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.2451 time to fit residues: 40.5834 Evaluate side-chains 94 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0050 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 122 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN B 204 HIS B 527 GLN B 585 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8792 Z= 0.162 Angle : 0.552 8.741 11868 Z= 0.283 Chirality : 0.039 0.146 1344 Planarity : 0.004 0.045 1506 Dihedral : 11.010 166.987 1267 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.30 % Allowed : 7.07 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.34 (0.26), residues: 1086 helix: 1.69 (0.21), residues: 610 sheet: -1.02 (0.51), residues: 90 loop : 0.22 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 213 HIS 0.008 0.001 HIS B 204 PHE 0.013 0.001 PHE B 275 TYR 0.019 0.001 TYR B 435 ARG 0.002 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: B 357 GLU cc_start: 0.6453 (mm-30) cc_final: 0.5978 (tt0) outliers start: 12 outliers final: 7 residues processed: 119 average time/residue: 0.2654 time to fit residues: 41.7031 Evaluate side-chains 102 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 0.0970 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 0.0870 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS B 331 GLN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8792 Z= 0.148 Angle : 0.505 7.252 11868 Z= 0.259 Chirality : 0.039 0.135 1344 Planarity : 0.004 0.044 1506 Dihedral : 9.697 170.491 1267 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.17 % Allowed : 10.00 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.26), residues: 1086 helix: 1.79 (0.21), residues: 610 sheet: -0.89 (0.52), residues: 90 loop : 0.28 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 213 HIS 0.002 0.001 HIS B 491 PHE 0.009 0.001 PHE A 178 TYR 0.018 0.001 TYR A 361 ARG 0.003 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 118 average time/residue: 0.2444 time to fit residues: 38.8446 Evaluate side-chains 105 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 93 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8792 Z= 0.138 Angle : 0.474 5.977 11868 Z= 0.245 Chirality : 0.038 0.136 1344 Planarity : 0.003 0.043 1506 Dihedral : 9.490 175.024 1266 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.07 % Allowed : 12.50 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1086 helix: 1.87 (0.21), residues: 614 sheet: -0.80 (0.52), residues: 90 loop : 0.18 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 213 HIS 0.006 0.001 HIS B 204 PHE 0.022 0.001 PHE B 508 TYR 0.017 0.001 TYR A 361 ARG 0.002 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.893 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 119 average time/residue: 0.2526 time to fit residues: 40.0033 Evaluate side-chains 106 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 ASN A 504 ASN B 204 HIS B 331 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8792 Z= 0.246 Angle : 0.573 7.188 11868 Z= 0.294 Chirality : 0.041 0.136 1344 Planarity : 0.004 0.042 1506 Dihedral : 9.527 178.098 1266 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.93 % Allowed : 13.80 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1086 helix: 1.52 (0.21), residues: 608 sheet: -1.09 (0.52), residues: 84 loop : 0.18 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 213 HIS 0.006 0.001 HIS B 563 PHE 0.018 0.002 PHE B 44 TYR 0.018 0.001 TYR A 361 ARG 0.003 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.935 Fit side-chains REVERT: A 321 MET cc_start: 0.6827 (ttp) cc_final: 0.6605 (mtp) outliers start: 27 outliers final: 22 residues processed: 112 average time/residue: 0.2637 time to fit residues: 39.1757 Evaluate side-chains 110 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8792 Z= 0.169 Angle : 0.512 6.496 11868 Z= 0.267 Chirality : 0.039 0.149 1344 Planarity : 0.004 0.051 1506 Dihedral : 9.345 179.345 1266 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.28 % Allowed : 15.00 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.26), residues: 1086 helix: 1.70 (0.21), residues: 610 sheet: -1.00 (0.53), residues: 90 loop : 0.14 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 391 HIS 0.007 0.001 HIS B 204 PHE 0.015 0.001 PHE B 44 TYR 0.016 0.001 TYR A 361 ARG 0.004 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.965 Fit side-chains REVERT: A 504 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.6978 (t0) outliers start: 21 outliers final: 14 residues processed: 111 average time/residue: 0.2717 time to fit residues: 39.8343 Evaluate side-chains 104 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.0000 chunk 76 optimal weight: 0.3980 chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8792 Z= 0.140 Angle : 0.487 5.719 11868 Z= 0.254 Chirality : 0.038 0.151 1344 Planarity : 0.003 0.051 1506 Dihedral : 9.195 179.190 1266 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.96 % Allowed : 15.11 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.26), residues: 1086 helix: 1.89 (0.21), residues: 610 sheet: -0.89 (0.53), residues: 90 loop : 0.19 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 391 HIS 0.006 0.001 HIS B 204 PHE 0.015 0.001 PHE B 44 TYR 0.015 0.001 TYR A 361 ARG 0.002 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.995 Fit side-chains REVERT: A 504 ASN cc_start: 0.7446 (OUTLIER) cc_final: 0.6948 (t0) REVERT: A 522 THR cc_start: 0.7426 (OUTLIER) cc_final: 0.6882 (t) outliers start: 18 outliers final: 13 residues processed: 105 average time/residue: 0.2613 time to fit residues: 36.5186 Evaluate side-chains 104 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8792 Z= 0.198 Angle : 0.542 8.486 11868 Z= 0.278 Chirality : 0.040 0.165 1344 Planarity : 0.004 0.050 1506 Dihedral : 9.251 179.577 1266 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.28 % Allowed : 15.33 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1086 helix: 1.70 (0.21), residues: 608 sheet: -1.00 (0.53), residues: 90 loop : 0.18 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 213 HIS 0.004 0.001 HIS B 563 PHE 0.011 0.001 PHE B 508 TYR 0.016 0.001 TYR A 361 ARG 0.003 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.966 Fit side-chains REVERT: B 302 SER cc_start: 0.7907 (t) cc_final: 0.7593 (p) outliers start: 21 outliers final: 16 residues processed: 107 average time/residue: 0.2571 time to fit residues: 36.4470 Evaluate side-chains 107 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.0170 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8792 Z= 0.160 Angle : 0.508 6.077 11868 Z= 0.262 Chirality : 0.039 0.164 1344 Planarity : 0.004 0.050 1506 Dihedral : 9.169 174.530 1266 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.07 % Allowed : 15.76 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.26), residues: 1086 helix: 1.84 (0.21), residues: 610 sheet: -0.95 (0.53), residues: 90 loop : 0.19 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 391 HIS 0.004 0.001 HIS B 204 PHE 0.011 0.001 PHE B 519 TYR 0.019 0.001 TYR A 406 ARG 0.002 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.996 Fit side-chains REVERT: A 522 THR cc_start: 0.7399 (OUTLIER) cc_final: 0.6838 (t) REVERT: B 263 LEU cc_start: 0.7243 (tp) cc_final: 0.7025 (tp) REVERT: B 283 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6519 (pt0) REVERT: B 302 SER cc_start: 0.7815 (t) cc_final: 0.7497 (p) outliers start: 19 outliers final: 14 residues processed: 106 average time/residue: 0.2579 time to fit residues: 36.7527 Evaluate side-chains 107 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.1980 chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.0470 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN B 204 HIS B 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8792 Z= 0.153 Angle : 0.503 5.911 11868 Z= 0.259 Chirality : 0.039 0.173 1344 Planarity : 0.003 0.050 1506 Dihedral : 9.095 172.915 1266 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.96 % Allowed : 16.30 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1086 helix: 1.91 (0.21), residues: 610 sheet: -0.95 (0.53), residues: 90 loop : 0.17 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 391 HIS 0.004 0.001 HIS B 204 PHE 0.010 0.001 PHE B 508 TYR 0.016 0.001 TYR A 406 ARG 0.002 0.000 ARG B 329 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.943 Fit side-chains REVERT: B 283 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6482 (pt0) REVERT: B 302 SER cc_start: 0.7790 (t) cc_final: 0.7473 (p) outliers start: 18 outliers final: 15 residues processed: 100 average time/residue: 0.2526 time to fit residues: 34.1500 Evaluate side-chains 104 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 79 optimal weight: 0.0030 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 0.0770 chunk 15 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 overall best weight: 0.2526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.227504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.201445 restraints weight = 8332.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.203632 restraints weight = 6724.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.204305 restraints weight = 5523.097| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8792 Z= 0.133 Angle : 0.484 6.796 11868 Z= 0.251 Chirality : 0.038 0.161 1344 Planarity : 0.003 0.047 1506 Dihedral : 8.962 171.548 1266 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.63 % Allowed : 16.63 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.26), residues: 1086 helix: 2.09 (0.21), residues: 612 sheet: -0.83 (0.54), residues: 90 loop : 0.24 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 391 HIS 0.004 0.000 HIS B 204 PHE 0.010 0.001 PHE B 508 TYR 0.017 0.001 TYR A 506 ARG 0.002 0.000 ARG B 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.51 seconds wall clock time: 31 minutes 46.79 seconds (1906.79 seconds total)