Starting phenix.real_space_refine on Wed Sep 25 05:38:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1r_15084/09_2024/8a1r_15084.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1r_15084/09_2024/8a1r_15084.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/8a1r_15084/09_2024/8a1r_15084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1r_15084/09_2024/8a1r_15084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1r_15084/09_2024/8a1r_15084.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1r_15084/09_2024/8a1r_15084.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= 0.000 sd= 0.001 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 48 5.16 5 C 5894 2.51 5 N 1554 2.21 5 O 1786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9286 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4530 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 571} Chain: "B" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4530 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 571} Chain: "A" Number of atoms: 113 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 83 Unusual residues: {'FAD': 1, 'KW2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Conformer: "B" Number of residues, atoms: 2, 83 Unusual residues: {'FAD': 1, 'KW2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} bond proxies already assigned to first conformer: 58 Chain: "B" Number of atoms: 113 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 83 Unusual residues: {'FAD': 1, 'KW2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Conformer: "B" Number of residues, atoms: 2, 83 Unusual residues: {'FAD': 1, 'KW2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} bond proxies already assigned to first conformer: 58 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AKW2 A 602 " occ=0.50 ... (58 atoms not shown) pdb=" O13BKW2 A 602 " occ=0.50 residue: pdb=" N AKW2 B 602 " occ=0.50 ... (58 atoms not shown) pdb=" O13BKW2 B 602 " occ=0.50 Time building chain proxies: 6.36, per 1000 atoms: 0.68 Number of scatterers: 9286 At special positions: 0 Unit cell: (101.905, 125.95, 92.745, 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 48 16.00 P 4 15.00 O 1786 8.00 N 1554 7.00 C 5894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 31 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 31 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 15 sheets defined 39.6% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 28 through 41 removed outlier: 3.594A pdb=" N LYS A 32 " --> pdb=" O CYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.532A pdb=" N LYS A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.950A pdb=" N VAL A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 181 removed outlier: 3.950A pdb=" N GLU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N HIS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.527A pdb=" N ILE A 190 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 219 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 485 through 494 Processing helix chain 'A' and resid 507 through 511 removed outlier: 3.682A pdb=" N THR A 511 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.516A pdb=" N ILE A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N MET A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.589A pdb=" N GLU A 576 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A 577 " --> pdb=" O CYS A 574 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 581 " --> pdb=" O PHE A 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 18 Processing helix chain 'B' and resid 28 through 41 removed outlier: 3.700A pdb=" N LYS B 32 " --> pdb=" O CYS B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 84 through 95 Processing helix chain 'B' and resid 96 through 102 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.749A pdb=" N VAL B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 178 Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 193 through 219 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 441 through 458 Processing helix chain 'B' and resid 485 through 494 Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 543 through 557 removed outlier: 4.065A pdb=" N ILE B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET B 557 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 Processing helix chain 'B' and resid 574 through 581 removed outlier: 3.736A pdb=" N LEU B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 3.598A pdb=" N LEU A 22 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N MET A 75 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 224 removed outlier: 6.396A pdb=" N ASP A 109 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE A 254 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 111 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 224 removed outlier: 6.396A pdb=" N ASP A 109 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE A 254 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 111 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.696A pdb=" N VAL A 312 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 289 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N MET A 315 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 291 " --> pdb=" O MET A 315 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 290 " --> pdb=" O ILE A 388 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 356 removed outlier: 6.874A pdb=" N LYS A 371 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 352 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 369 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN A 354 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU A 367 " --> pdb=" O GLN A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 473 removed outlier: 3.596A pdb=" N LYS A 523 " --> pdb=" O HIS A 538 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS A 520 " --> pdb=" O PHE A 505 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 498 through 499 Processing sheet with id=AA9, first strand: chain 'B' and resid 46 through 49 removed outlier: 7.359A pdb=" N MET B 75 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 82 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 222 through 224 removed outlier: 3.518A pdb=" N THR B 222 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 224 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA B 134 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 110 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU B 136 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 112 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP B 109 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 229 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 222 through 224 removed outlier: 3.518A pdb=" N THR B 222 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 224 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA B 134 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 110 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU B 136 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 112 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP B 109 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AB4, first strand: chain 'B' and resid 274 through 275 removed outlier: 6.745A pdb=" N ILE B 274 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 347 through 354 removed outlier: 5.563A pdb=" N HIS B 373 " --> pdb=" O PRO B 349 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 471 through 473 removed outlier: 6.515A pdb=" N VAL B 525 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 537 " --> pdb=" O LYS B 523 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS B 523 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL B 539 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR B 521 " --> pdb=" O VAL B 539 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1176 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: 3.37 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2976 1.34 - 1.46: 1903 1.46 - 1.58: 4524 1.58 - 1.69: 17 1.69 - 1.81: 66 Bond restraints: 9486 Sorted by residual: bond pdb=" C12BKW2 B 602 " pdb=" C13BKW2 B 602 " ideal model delta sigma weight residual 1.551 1.228 0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" C12AKW2 A 602 " pdb=" C13AKW2 A 602 " ideal model delta sigma weight residual 1.551 1.229 0.322 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C12AKW2 B 602 " pdb=" C13AKW2 B 602 " ideal model delta sigma weight residual 1.551 1.229 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" C12BKW2 A 602 " pdb=" C13BKW2 A 602 " ideal model delta sigma weight residual 1.551 1.230 0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" C13BKW2 A 602 " pdb=" C14BKW2 A 602 " ideal model delta sigma weight residual 1.557 1.369 0.188 2.00e-02 2.50e+03 8.87e+01 ... (remaining 9481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 12837 4.70 - 9.41: 57 9.41 - 14.11: 0 14.11 - 18.81: 0 18.81 - 23.52: 4 Bond angle restraints: 12898 Sorted by residual: angle pdb=" C12BKW2 B 602 " pdb=" C13BKW2 B 602 " pdb=" C14BKW2 B 602 " ideal model delta sigma weight residual 85.19 108.71 -23.52 3.00e+00 1.11e-01 6.15e+01 angle pdb=" C12BKW2 A 602 " pdb=" C13BKW2 A 602 " pdb=" C14BKW2 A 602 " ideal model delta sigma weight residual 85.19 108.71 -23.52 3.00e+00 1.11e-01 6.14e+01 angle pdb=" C12AKW2 A 602 " pdb=" C13AKW2 A 602 " pdb=" C14AKW2 A 602 " ideal model delta sigma weight residual 85.19 108.62 -23.43 3.00e+00 1.11e-01 6.10e+01 angle pdb=" C12AKW2 B 602 " pdb=" C13AKW2 B 602 " pdb=" C14AKW2 B 602 " ideal model delta sigma weight residual 85.19 108.46 -23.27 3.00e+00 1.11e-01 6.02e+01 angle pdb=" CA CYS B 520 " pdb=" C CYS B 520 " pdb=" O CYS B 520 " ideal model delta sigma weight residual 121.55 117.92 3.63 1.06e+00 8.90e-01 1.17e+01 ... (remaining 12893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 5657 34.56 - 69.12: 144 69.12 - 103.68: 11 103.68 - 138.24: 4 138.24 - 172.80: 4 Dihedral angle restraints: 5820 sinusoidal: 2446 harmonic: 3374 Sorted by residual: dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual -86.00 -131.26 45.26 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -130.91 44.91 1 1.00e+01 1.00e-02 2.80e+01 dihedral pdb=" O5' FAD B 601 " pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " pdb=" PA FAD B 601 " ideal model delta sinusoidal sigma weight residual -61.77 111.03 -172.80 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 5817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1423 0.111 - 0.221: 43 0.221 - 0.332: 0 0.332 - 0.442: 2 0.442 - 0.553: 10 Chirality restraints: 1478 Sorted by residual: chirality pdb=" C12AKW2 B 602 " pdb=" C13AKW2 B 602 " pdb=" C17AKW2 B 602 " pdb=" C18AKW2 B 602 " both_signs ideal model delta sigma weight residual False 3.20 2.65 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" C12AKW2 A 602 " pdb=" C13AKW2 A 602 " pdb=" C17AKW2 A 602 " pdb=" C18AKW2 A 602 " both_signs ideal model delta sigma weight residual False 3.20 2.65 0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" C12BKW2 B 602 " pdb=" C13BKW2 B 602 " pdb=" C17BKW2 B 602 " pdb=" C18BKW2 B 602 " both_signs ideal model delta sigma weight residual False 3.20 2.65 0.54 2.00e-01 2.50e+01 7.42e+00 ... (remaining 1475 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 142 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 143 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 590 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO B 591 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 591 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 591 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 232 " 0.031 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 233 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " 0.025 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 161 2.66 - 3.22: 9109 3.22 - 3.78: 15142 3.78 - 4.34: 20511 4.34 - 4.90: 32842 Nonbonded interactions: 77765 Sorted by model distance: nonbonded pdb=" OG1 THR B 573 " pdb=" OE1 GLU B 576 " model vdw 2.097 3.040 nonbonded pdb=" OG1 THR A 475 " pdb=" O LEU A 477 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR B 423 " pdb=" O VAL B 428 " model vdw 2.210 3.040 nonbonded pdb=" O ARG B 322 " pdb=" O1 BKW2 B 602 " model vdw 2.211 3.040 nonbonded pdb=" O ARG A 322 " pdb=" O1 BKW2 A 602 " model vdw 2.251 3.040 ... (remaining 77760 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' and (resid 6 through 598 or resid 601)) selection = (chain 'B' and (resid 6 through 598 or resid 601)) } 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=0.50 max=1.00 mean=0.99 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: 2.540 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: 0.090 Process input model: 25.060 Find NCS groups from input model: 0.360 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.011 0.323 9486 Z= 0.767 Angle : 0.859 23.517 12898 Z= 0.378 Chirality : 0.065 0.553 1478 Planarity : 0.004 0.052 1606 Dihedral : 16.562 172.797 3664 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.06 (0.25), residues: 1182 helix: 1.46 (0.27), residues: 400 sheet: -0.61 (0.35), residues: 238 loop : -0.86 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 194 HIS 0.005 0.001 HIS A 502 PHE 0.017 0.002 PHE B 578 TYR 0.017 0.001 TYR B 429 ARG 0.005 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 MET cc_start: 0.8239 (mpp) cc_final: 0.7874 (mpp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2479 time to fit residues: 31.3224 Evaluate side-chains 62 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.0570 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS A 435 ASN B 225 ASN B 468 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9486 Z= 0.334 Angle : 0.692 10.589 12898 Z= 0.352 Chirality : 0.046 0.153 1478 Planarity : 0.005 0.050 1606 Dihedral : 12.473 176.764 1564 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.91 % Allowed : 8.33 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.25 (0.25), residues: 1182 helix: 1.10 (0.25), residues: 404 sheet: -1.08 (0.34), residues: 236 loop : -0.61 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.006 0.001 HIS A 502 PHE 0.025 0.002 PHE A 304 TYR 0.021 0.002 TYR B 91 ARG 0.004 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 592 ILE cc_start: 0.8974 (mm) cc_final: 0.8667 (mp) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.2440 time to fit residues: 26.5341 Evaluate side-chains 60 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 47 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 468 ASN B 209 ASN B 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9486 Z= 0.333 Angle : 0.699 10.762 12898 Z= 0.353 Chirality : 0.045 0.152 1478 Planarity : 0.005 0.051 1606 Dihedral : 12.007 176.578 1564 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.03 % Allowed : 12.30 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.49 (0.25), residues: 1182 helix: 0.76 (0.25), residues: 406 sheet: -1.13 (0.34), residues: 236 loop : -0.67 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.007 0.002 HIS A 339 PHE 0.030 0.002 PHE B 304 TYR 0.023 0.002 TYR B 91 ARG 0.007 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.9005 (m-80) cc_final: 0.8516 (m-80) REVERT: B 336 MET cc_start: 0.8455 (mpp) cc_final: 0.8198 (mpp) REVERT: B 557 MET cc_start: 0.8189 (ppp) cc_final: 0.7874 (ppp) outliers start: 20 outliers final: 13 residues processed: 78 average time/residue: 0.2174 time to fit residues: 24.3784 Evaluate side-chains 70 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9486 Z= 0.235 Angle : 0.621 9.774 12898 Z= 0.314 Chirality : 0.044 0.136 1478 Planarity : 0.004 0.053 1606 Dihedral : 11.667 175.604 1564 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.73 % Allowed : 13.82 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.45 (0.25), residues: 1182 helix: 0.82 (0.25), residues: 406 sheet: -1.08 (0.34), residues: 234 loop : -0.70 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.006 0.001 HIS A 173 PHE 0.023 0.002 PHE A 304 TYR 0.013 0.001 TYR B 92 ARG 0.003 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.9022 (m-80) cc_final: 0.8507 (m-80) REVERT: B 557 MET cc_start: 0.8027 (ppp) cc_final: 0.7721 (ppp) REVERT: B 592 ILE cc_start: 0.8926 (mm) cc_final: 0.8661 (mp) outliers start: 17 outliers final: 13 residues processed: 72 average time/residue: 0.2118 time to fit residues: 22.5585 Evaluate side-chains 69 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 555 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 1 optimal weight: 0.0970 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 58 optimal weight: 0.0050 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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: 0.7850 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9486 Z= 0.178 Angle : 0.604 9.567 12898 Z= 0.302 Chirality : 0.045 0.146 1478 Planarity : 0.004 0.054 1606 Dihedral : 11.329 175.158 1564 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.83 % Allowed : 15.24 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.39 (0.25), residues: 1182 helix: 0.89 (0.25), residues: 406 sheet: -0.90 (0.33), residues: 242 loop : -0.75 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.004 0.001 HIS A 502 PHE 0.048 0.002 PHE B 304 TYR 0.039 0.001 TYR A 91 ARG 0.003 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.8716 (p0) cc_final: 0.8291 (m-30) REVERT: B 23 PHE cc_start: 0.8993 (m-80) cc_final: 0.8493 (m-80) REVERT: B 336 MET cc_start: 0.8222 (mpp) cc_final: 0.7968 (mpp) REVERT: B 557 MET cc_start: 0.7704 (ppp) cc_final: 0.7343 (ppp) outliers start: 18 outliers final: 12 residues processed: 73 average time/residue: 0.2075 time to fit residues: 22.4219 Evaluate side-chains 67 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 66 optimal weight: 0.1980 chunk 28 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9486 Z= 0.269 Angle : 0.658 11.665 12898 Z= 0.331 Chirality : 0.044 0.163 1478 Planarity : 0.004 0.053 1606 Dihedral : 11.211 175.159 1564 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.24 % Allowed : 16.16 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.43 (0.25), residues: 1182 helix: 0.79 (0.25), residues: 408 sheet: -0.88 (0.33), residues: 240 loop : -0.75 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 10 HIS 0.005 0.001 HIS A 339 PHE 0.030 0.002 PHE B 76 TYR 0.038 0.002 TYR A 91 ARG 0.003 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.9322 (mttt) cc_final: 0.9096 (mmtt) REVERT: B 23 PHE cc_start: 0.9004 (m-80) cc_final: 0.8509 (m-80) outliers start: 22 outliers final: 14 residues processed: 75 average time/residue: 0.2301 time to fit residues: 24.9132 Evaluate side-chains 72 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN B 166 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9486 Z= 0.177 Angle : 0.628 9.777 12898 Z= 0.314 Chirality : 0.045 0.191 1478 Planarity : 0.004 0.053 1606 Dihedral : 11.064 174.388 1564 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.42 % Allowed : 17.38 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.32 (0.25), residues: 1182 helix: 0.83 (0.25), residues: 408 sheet: -0.79 (0.33), residues: 240 loop : -0.65 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 10 HIS 0.004 0.001 HIS A 339 PHE 0.031 0.002 PHE B 304 TYR 0.036 0.001 TYR A 91 ARG 0.003 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.8709 (p0) cc_final: 0.8284 (m-30) REVERT: B 10 TRP cc_start: 0.8195 (m-10) cc_final: 0.7981 (m-10) REVERT: B 23 PHE cc_start: 0.8958 (m-80) cc_final: 0.8513 (m-80) outliers start: 14 outliers final: 11 residues processed: 73 average time/residue: 0.2250 time to fit residues: 23.3883 Evaluate side-chains 69 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 72 optimal weight: 0.0570 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 89 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 overall best weight: 2.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9486 Z= 0.299 Angle : 0.686 10.300 12898 Z= 0.349 Chirality : 0.046 0.242 1478 Planarity : 0.005 0.052 1606 Dihedral : 11.110 174.675 1564 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.73 % Allowed : 18.19 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.41 (0.25), residues: 1182 helix: 0.72 (0.25), residues: 408 sheet: -0.82 (0.33), residues: 240 loop : -0.69 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.005 0.002 HIS A 339 PHE 0.071 0.002 PHE B 304 TYR 0.045 0.002 TYR A 91 ARG 0.005 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.8959 (m-80) cc_final: 0.8482 (m-80) outliers start: 17 outliers final: 15 residues processed: 71 average time/residue: 0.2113 time to fit residues: 21.9974 Evaluate side-chains 70 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.7936 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9486 Z= 0.246 Angle : 0.669 10.376 12898 Z= 0.339 Chirality : 0.046 0.254 1478 Planarity : 0.004 0.052 1606 Dihedral : 11.071 174.056 1564 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.63 % Allowed : 18.50 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.42 (0.25), residues: 1182 helix: 0.70 (0.25), residues: 404 sheet: -0.87 (0.33), residues: 238 loop : -0.65 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.004 0.001 HIS A 339 PHE 0.040 0.002 PHE B 304 TYR 0.042 0.002 TYR A 91 ARG 0.004 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.8949 (m-80) cc_final: 0.8460 (m-80) outliers start: 16 outliers final: 14 residues processed: 69 average time/residue: 0.1924 time to fit residues: 19.8860 Evaluate side-chains 71 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.7881 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9486 Z= 0.182 Angle : 0.650 10.695 12898 Z= 0.328 Chirality : 0.046 0.223 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.940 173.623 1564 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.63 % Allowed : 19.00 % Favored : 79.37 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 9.52 % 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: -0.34 (0.25), residues: 1182 helix: 0.70 (0.25), residues: 404 sheet: -0.77 (0.33), residues: 240 loop : -0.57 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 10 HIS 0.004 0.001 HIS A 502 PHE 0.025 0.002 PHE B 304 TYR 0.044 0.001 TYR A 91 ARG 0.003 0.000 ARG A 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.8908 (m-80) cc_final: 0.8432 (m-80) outliers start: 16 outliers final: 13 residues processed: 72 average time/residue: 0.1967 time to fit residues: 21.2251 Evaluate side-chains 69 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.041023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.029749 restraints weight = 85512.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.030598 restraints weight = 60045.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.031205 restraints weight = 46737.092| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9486 Z= 0.248 Angle : 0.690 12.593 12898 Z= 0.347 Chirality : 0.046 0.313 1478 Planarity : 0.004 0.052 1606 Dihedral : 10.946 173.444 1564 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.63 % Allowed : 18.90 % Favored : 79.47 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 9.52 % 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: -0.38 (0.25), residues: 1182 helix: 0.64 (0.26), residues: 404 sheet: -0.75 (0.33), residues: 240 loop : -0.59 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 10 HIS 0.005 0.001 HIS B 166 PHE 0.075 0.002 PHE B 304 TYR 0.043 0.002 TYR A 91 ARG 0.003 0.000 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1805.28 seconds wall clock time: 33 minutes 51.55 seconds (2031.55 seconds total)