Starting phenix.real_space_refine on Fri Jul 19 19:09:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/07_2024/8phf_17660.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/07_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_17660/07_2024/8phf_17660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/07_2024/8phf_17660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/07_2024/8phf_17660.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/07_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 Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.29, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 3.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.78 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: 2.39 Time building geometry restraints manager: 3.93 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: 99.35 - 106.30: 182 106.30 - 113.25: 4799 113.25 - 120.20: 3331 120.20 - 127.15: 3489 127.15 - 134.10: 67 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 2.520 nonbonded pdb=" OG SER B 60 " pdb=" OE1 GLU B 63 " model vdw 2.143 2.440 nonbonded pdb=" OG SER A 60 " pdb=" OD1 ASP A 62 " model vdw 2.191 2.440 nonbonded pdb=" O3' FAD B 701 " pdb=" O5' FAD B 701 " model vdw 2.260 2.440 nonbonded pdb=" OD2 ASP A 201 " pdb=" NZ LYS A 203 " model vdw 2.261 2.520 ... (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 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: 0.890 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.360 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.740 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.958 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: 0.2353 time to fit residues: 39.0872 Evaluate side-chains 94 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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: 0.2980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.0010 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 277 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN B 122 ASN B 161 GLN B 204 HIS B 527 GLN B 585 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.1361 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= 0.158 Angle : 0.540 9.326 11868 Z= 0.275 Chirality : 0.039 0.150 1344 Planarity : 0.004 0.045 1506 Dihedral : 11.184 172.780 1267 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.30 % Allowed : 6.85 % Favored : 91.85 % 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: 1.40 (0.26), residues: 1086 helix: 1.70 (0.21), residues: 610 sheet: -0.51 (0.47), residues: 114 loop : 0.22 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 213 HIS 0.008 0.001 HIS B 204 PHE 0.013 0.001 PHE B 519 TYR 0.019 0.001 TYR B 435 ARG 0.004 0.000 ARG A 609 *********************** 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 120 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.013 Fit side-chains REVERT: B 329 ARG cc_start: 0.5558 (mmm-85) cc_final: 0.5291 (mmm-85) REVERT: B 619 ARG cc_start: 0.7407 (ttm-80) cc_final: 0.7100 (ttm-80) outliers start: 12 outliers final: 7 residues processed: 115 average time/residue: 0.2420 time to fit residues: 37.4295 Evaluate side-chains 101 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 558 LEU 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: 0.9980 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 78 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS B 216 ASN ** 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: 0.6754 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8792 Z= 0.169 Angle : 0.506 7.835 11868 Z= 0.260 Chirality : 0.039 0.136 1344 Planarity : 0.004 0.044 1506 Dihedral : 9.826 179.484 1267 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.07 % Allowed : 10.43 % Favored : 87.50 % 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: 1.42 (0.26), residues: 1086 helix: 1.73 (0.21), residues: 610 sheet: -0.87 (0.52), residues: 90 loop : 0.26 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 213 HIS 0.003 0.001 HIS B 563 PHE 0.010 0.001 PHE A 178 TYR 0.016 0.001 TYR A 361 ARG 0.006 0.000 ARG B 317 *********************** 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 123 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 241 LYS cc_start: 0.7230 (mmtt) cc_final: 0.7004 (mmmm) REVERT: B 619 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7106 (ttm-80) outliers start: 19 outliers final: 12 residues processed: 116 average time/residue: 0.2310 time to fit residues: 36.3617 Evaluate side-chains 108 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 516 LEU 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 544 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: 0.7980 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 204 HIS A 504 ASN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6800 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8792 Z= 0.189 Angle : 0.508 7.891 11868 Z= 0.262 Chirality : 0.039 0.138 1344 Planarity : 0.004 0.042 1506 Dihedral : 9.526 175.410 1266 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.61 % Allowed : 12.93 % Favored : 84.46 % 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: 1.60 (0.21), residues: 620 sheet: -0.95 (0.53), residues: 84 loop : 0.26 (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 0.012 0.001 PHE B 44 TYR 0.016 0.001 TYR A 361 ARG 0.005 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 118 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 198 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6242 (tt) REVERT: B 516 LEU cc_start: 0.8145 (mm) cc_final: 0.7904 (mm) REVERT: B 619 ARG cc_start: 0.7415 (ttm-80) cc_final: 0.7114 (ttm-80) outliers start: 24 outliers final: 19 residues processed: 108 average time/residue: 0.2196 time to fit residues: 32.6618 Evaluate side-chains 109 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU 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 425 PHE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 516 LEU 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 327 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 585 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8792 Z= 0.193 Angle : 0.502 6.303 11868 Z= 0.261 Chirality : 0.039 0.134 1344 Planarity : 0.004 0.041 1506 Dihedral : 9.370 173.497 1266 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.72 % Allowed : 14.13 % Favored : 83.15 % 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: 1.27 (0.26), residues: 1086 helix: 1.56 (0.21), residues: 620 sheet: -1.02 (0.53), residues: 84 loop : 0.26 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 391 HIS 0.007 0.001 HIS B 204 PHE 0.014 0.001 PHE B 44 TYR 0.016 0.001 TYR A 361 ARG 0.005 0.000 ARG B 317 *********************** 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 119 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 198 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6260 (tt) REVERT: B 80 GLU cc_start: 0.6829 (pt0) cc_final: 0.6612 (pt0) REVERT: B 516 LEU cc_start: 0.8126 (mm) cc_final: 0.7854 (mm) REVERT: B 619 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.7120 (ttm-80) outliers start: 25 outliers final: 20 residues processed: 110 average time/residue: 0.2370 time to fit residues: 35.8947 Evaluate side-chains 109 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU 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 368 ASP Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain B residue 87 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 327 CYS 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: 1.9990 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2162 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= 0.206 Angle : 0.510 6.256 11868 Z= 0.265 Chirality : 0.039 0.136 1344 Planarity : 0.004 0.039 1506 Dihedral : 9.337 172.817 1266 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.15 % Allowed : 14.67 % 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: 1.25 (0.26), residues: 1086 helix: 1.61 (0.21), residues: 610 sheet: -1.08 (0.53), residues: 84 loop : 0.16 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 391 HIS 0.006 0.001 HIS B 204 PHE 0.015 0.001 PHE B 44 TYR 0.016 0.001 TYR A 361 ARG 0.005 0.000 ARG B 317 *********************** 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 121 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 1.005 Fit side-chains REVERT: A 198 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6325 (tt) REVERT: B 516 LEU cc_start: 0.8140 (mm) cc_final: 0.7860 (mm) REVERT: B 619 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.7147 (ttm-80) outliers start: 29 outliers final: 22 residues processed: 109 average time/residue: 0.2502 time to fit residues: 36.9378 Evaluate side-chains 111 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 198 LEU 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 309 SER 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 429 ASN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 516 LEU 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 327 CYS 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=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: 0.0050 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8792 Z= 0.180 Angle : 0.511 8.088 11868 Z= 0.266 Chirality : 0.039 0.141 1344 Planarity : 0.003 0.038 1506 Dihedral : 9.201 171.770 1266 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.83 % Allowed : 15.11 % Favored : 82.07 % 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: 1.26 (0.26), residues: 1086 helix: 1.67 (0.21), residues: 612 sheet: -1.01 (0.53), residues: 90 loop : 0.06 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 391 HIS 0.006 0.001 HIS B 204 PHE 0.014 0.001 PHE B 44 TYR 0.015 0.001 TYR A 361 ARG 0.005 0.000 ARG B 317 *********************** 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 120 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.6971 (tpt) cc_final: 0.6661 (tpt) REVERT: A 198 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6022 (tt) REVERT: B 516 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7920 (mm) REVERT: B 619 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7152 (ttm-80) outliers start: 26 outliers final: 19 residues processed: 110 average time/residue: 0.2424 time to fit residues: 36.1105 Evaluate side-chains 109 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU 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 309 SER 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 429 ASN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 516 LEU 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 327 CYS Chi-restraints excluded: chain B residue 516 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8792 Z= 0.194 Angle : 0.521 6.286 11868 Z= 0.270 Chirality : 0.040 0.142 1344 Planarity : 0.003 0.038 1506 Dihedral : 9.192 172.430 1266 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.72 % Allowed : 15.76 % Favored : 81.52 % 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: 1.20 (0.26), residues: 1086 helix: 1.61 (0.21), residues: 612 sheet: -1.07 (0.53), residues: 90 loop : 0.07 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 213 HIS 0.007 0.001 HIS B 204 PHE 0.016 0.001 PHE B 44 TYR 0.016 0.001 TYR A 406 ARG 0.005 0.000 ARG B 317 *********************** 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 fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 198 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6070 (tt) REVERT: B 516 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7901 (mm) REVERT: B 619 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.7164 (ttm-80) outliers start: 25 outliers final: 20 residues processed: 105 average time/residue: 0.2606 time to fit residues: 36.4089 Evaluate side-chains 112 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU 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 309 SER 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 429 ASN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 516 LEU 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 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 516 LEU 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: 2.9990 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8792 Z= 0.353 Angle : 0.669 8.446 11868 Z= 0.343 Chirality : 0.044 0.169 1344 Planarity : 0.004 0.038 1506 Dihedral : 9.672 176.923 1266 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.93 % Allowed : 15.65 % Favored : 81.41 % 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: 0.59 (0.26), residues: 1086 helix: 1.01 (0.21), residues: 616 sheet: -0.71 (0.45), residues: 120 loop : -0.09 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 213 HIS 0.006 0.002 HIS B 204 PHE 0.019 0.002 PHE A 178 TYR 0.020 0.002 TYR A 361 ARG 0.005 0.001 ARG B 304 *********************** 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 122 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.948 Fit side-chains REVERT: A 124 MET cc_start: 0.7199 (tpt) cc_final: 0.6843 (tpt) REVERT: A 198 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6537 (tt) REVERT: A 425 PHE cc_start: 0.6429 (OUTLIER) cc_final: 0.6173 (t80) REVERT: B 142 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7081 (mp) REVERT: B 516 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7912 (mm) REVERT: B 619 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.7202 (ttm-80) outliers start: 27 outliers final: 17 residues processed: 109 average time/residue: 0.2614 time to fit residues: 38.1324 Evaluate side-chains 108 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 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 544 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 516 LEU 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: 0.9980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 0.0010 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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: 0.6848 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8792 Z= 0.177 Angle : 0.535 7.177 11868 Z= 0.274 Chirality : 0.040 0.184 1344 Planarity : 0.003 0.037 1506 Dihedral : 9.285 175.091 1266 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.07 % Allowed : 17.07 % Favored : 80.87 % 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: 0.97 (0.26), residues: 1086 helix: 1.43 (0.21), residues: 618 sheet: -1.25 (0.53), residues: 90 loop : -0.03 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 391 HIS 0.007 0.001 HIS B 204 PHE 0.009 0.001 PHE A 178 TYR 0.015 0.001 TYR A 406 ARG 0.005 0.000 ARG B 317 ********************** 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 fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.6988 (tpt) cc_final: 0.6667 (tpt) REVERT: A 198 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6096 (tt) REVERT: A 430 GLU cc_start: 0.6490 (tp30) cc_final: 0.6020 (tp30) REVERT: B 142 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6886 (mp) REVERT: B 516 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7817 (mm) REVERT: B 619 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.7226 (ttm-80) outliers start: 19 outliers final: 14 residues processed: 101 average time/residue: 0.2533 time to fit residues: 34.0620 Evaluate side-chains 102 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 327 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.218929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.191974 restraints weight = 8541.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.195467 restraints weight = 6328.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.197537 restraints weight = 5125.500| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.2696 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= 0.159 Angle : 0.529 11.960 11868 Z= 0.268 Chirality : 0.040 0.179 1344 Planarity : 0.003 0.038 1506 Dihedral : 9.166 175.152 1266 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.96 % Allowed : 16.96 % Favored : 81.09 % 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: 1.30 (0.26), residues: 1086 helix: 1.70 (0.21), residues: 616 sheet: -0.53 (0.48), residues: 110 loop : -0.01 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 391 HIS 0.008 0.001 HIS B 204 PHE 0.008 0.001 PHE A 425 TYR 0.015 0.001 TYR A 406 ARG 0.005 0.000 ARG B 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.25 seconds wall clock time: 30 minutes 55.16 seconds (1855.16 seconds total)