Starting phenix.real_space_refine on Mon Apr 8 12:50:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoh_33348/04_2024/7xoh_33348_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoh_33348/04_2024/7xoh_33348.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/7xoh_33348/04_2024/7xoh_33348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoh_33348/04_2024/7xoh_33348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoh_33348/04_2024/7xoh_33348_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoh_33348/04_2024/7xoh_33348_trim_updated.pdb" } 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= 0.011 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 60 5.16 5 C 8484 2.51 5 N 2336 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13524 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "A" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "C" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "D" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 7.06, per 1000 atoms: 0.52 Number of scatterers: 13524 At special positions: 0 Unit cell: (84.53, 146.59, 84.53, 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 60 16.00 P 4 15.00 O 2640 8.00 N 2336 7.00 C 8484 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.00 Conformation dependent library (CDL) restraints added in 2.5 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 15 sheets defined 31.3% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'B' and resid 7 through 9 No H-bonds generated for 'chain 'B' and resid 7 through 9' Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 74 through 86 removed outlier: 3.751A pdb=" N GLY B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 151 through 159 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 188 through 197 removed outlier: 3.545A pdb=" N TYR B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 268 through 280 Processing helix chain 'B' and resid 300 through 303 removed outlier: 4.342A pdb=" N SER B 303 " --> pdb=" O GLY B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 330 through 333 No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 391 through 394 No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 423 through 430 Processing helix chain 'B' and resid 450 through 459 Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 75 through 86 removed outlier: 4.158A pdb=" N ARG A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.680A pdb=" N THR A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.792A pdb=" N GLY A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 268 through 280 Processing helix chain 'A' and resid 310 through 313 No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 330 through 333 No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 393 through 396 No H-bonds generated for 'chain 'A' and resid 393 through 396' Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 423 through 430 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 44 through 57 removed outlier: 3.968A pdb=" N VAL C 49 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.676A pdb=" N GLY C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 151 through 159 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 185 through 195 Processing helix chain 'C' and resid 248 through 261 Processing helix chain 'C' and resid 268 through 280 Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 310 through 313 No H-bonds generated for 'chain 'C' and resid 310 through 313' Processing helix chain 'C' and resid 330 through 333 No H-bonds generated for 'chain 'C' and resid 330 through 333' Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 391 through 394 No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 423 through 431 removed outlier: 4.092A pdb=" N ARG C 431 " --> pdb=" O GLY C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 removed outlier: 3.511A pdb=" N GLY C 455 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.802A pdb=" N LYS D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 86 removed outlier: 4.141A pdb=" N ARG D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 128 through 138 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 162 through 169 removed outlier: 3.704A pdb=" N THR D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 195 Processing helix chain 'D' and resid 248 through 261 Processing helix chain 'D' and resid 268 through 280 Processing helix chain 'D' and resid 330 through 333 No H-bonds generated for 'chain 'D' and resid 330 through 333' Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.685A pdb=" N TYR D 363 " --> pdb=" O ILE D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 423 through 431 removed outlier: 4.251A pdb=" N ARG D 431 " --> pdb=" O GLY D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 457 removed outlier: 3.591A pdb=" N GLY D 455 " --> pdb=" O TYR D 451 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 16 through 19 removed outlier: 4.778A pdb=" N VAL B 30 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 66 through 69 removed outlier: 6.296A pdb=" N LYS B 89 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLU B 69 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 91 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU B 112 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N CYS B 94 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL B 114 " --> pdb=" O CYS B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 367 through 370 removed outlier: 3.506A pdb=" N GLY B 384 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 416 through 418 removed outlier: 8.101A pdb=" N ILE B 417 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N MET B 437 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 16 through 18 Processing sheet with id= F, first strand: chain 'A' and resid 66 through 69 removed outlier: 6.749A pdb=" N LYS A 89 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLU A 69 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A 91 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 114 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.619A pdb=" N GLY A 384 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 416 through 418 removed outlier: 8.125A pdb=" N ILE A 417 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N MET A 437 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 17 through 19 removed outlier: 4.806A pdb=" N VAL C 30 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 66 through 69 removed outlier: 6.277A pdb=" N LYS C 89 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU C 69 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 91 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU C 112 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N CYS C 94 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL C 114 " --> pdb=" O CYS C 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 416 through 418 removed outlier: 8.043A pdb=" N ILE C 417 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N MET C 437 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 16 through 18 Processing sheet with id= M, first strand: chain 'D' and resid 66 through 69 removed outlier: 6.774A pdb=" N LYS D 89 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLU D 69 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL D 91 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 114 " --> pdb=" O PHE D 92 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 367 through 370 removed outlier: 3.521A pdb=" N GLY D 384 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 416 through 418 removed outlier: 8.096A pdb=" N ILE D 417 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N MET D 437 " --> pdb=" O ILE D 417 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1023 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: 3.97 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4589 1.34 - 1.46: 2670 1.46 - 1.58: 6429 1.58 - 1.69: 4 1.69 - 1.81: 104 Bond restraints: 13796 Sorted by residual: bond pdb=" CA GLY A 297 " pdb=" C GLY A 297 " ideal model delta sigma weight residual 1.520 1.486 0.034 7.30e-03 1.88e+04 2.23e+01 bond pdb=" N ILE A 180 " pdb=" CA ILE A 180 " ideal model delta sigma weight residual 1.457 1.492 -0.036 1.15e-02 7.56e+03 9.63e+00 bond pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.69e+00 bond pdb=" N ASP C 45 " pdb=" CA ASP C 45 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.04e+00 bond pdb=" N THR C 182 " pdb=" CA THR C 182 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.72e+00 ... (remaining 13791 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.34: 539 106.34 - 113.25: 7439 113.25 - 120.17: 4895 120.17 - 127.08: 5720 127.08 - 133.99: 175 Bond angle restraints: 18768 Sorted by residual: angle pdb=" N SER D 313 " pdb=" CA SER D 313 " pdb=" C SER D 313 " ideal model delta sigma weight residual 112.54 105.53 7.01 1.22e+00 6.72e-01 3.30e+01 angle pdb=" N GLY C 183 " pdb=" CA GLY C 183 " pdb=" C GLY C 183 " ideal model delta sigma weight residual 114.46 108.38 6.08 1.81e+00 3.05e-01 1.13e+01 angle pdb=" C LYS C 44 " pdb=" N ASP C 45 " pdb=" CA ASP C 45 " ideal model delta sigma weight residual 120.38 116.06 4.32 1.37e+00 5.33e-01 9.94e+00 angle pdb=" N SER C 43 " pdb=" CA SER C 43 " pdb=" C SER C 43 " ideal model delta sigma weight residual 113.23 109.44 3.79 1.24e+00 6.50e-01 9.34e+00 angle pdb=" C GLN B 367 " pdb=" N MET B 368 " pdb=" CA MET B 368 " ideal model delta sigma weight residual 122.08 116.81 5.27 1.83e+00 2.99e-01 8.28e+00 ... (remaining 18763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.33: 7832 22.33 - 44.65: 324 44.65 - 66.98: 51 66.98 - 89.30: 11 89.30 - 111.63: 2 Dihedral angle restraints: 8220 sinusoidal: 3124 harmonic: 5096 Sorted by residual: dihedral pdb=" C5A PLP D 501 " pdb=" O4P PLP D 501 " pdb=" P PLP D 501 " pdb=" O1P PLP D 501 " ideal model delta sinusoidal sigma weight residual 76.43 -171.94 -111.63 1 2.00e+01 2.50e-03 3.28e+01 dihedral pdb=" C5A PLP C 501 " pdb=" O4P PLP C 501 " pdb=" P PLP C 501 " pdb=" O1P PLP C 501 " ideal model delta sinusoidal sigma weight residual 76.43 177.79 -101.36 1 2.00e+01 2.50e-03 2.87e+01 dihedral pdb=" C5 PLP B 501 " pdb=" C5A PLP B 501 " pdb=" O4P PLP B 501 " pdb=" P PLP B 501 " ideal model delta sinusoidal sigma weight residual 188.31 117.64 70.66 1 2.00e+01 2.50e-03 1.61e+01 ... (remaining 8217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1325 0.035 - 0.070: 524 0.070 - 0.105: 205 0.105 - 0.140: 48 0.140 - 0.175: 2 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CA ILE A 180 " pdb=" N ILE A 180 " pdb=" C ILE A 180 " pdb=" CB ILE A 180 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE C 47 " pdb=" N ILE C 47 " pdb=" C ILE C 47 " pdb=" CB ILE C 47 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 2101 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 180 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C ILE C 180 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE C 180 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY C 181 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 294 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO B 295 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 313 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C SER C 313 " 0.027 2.00e-02 2.50e+03 pdb=" O SER C 313 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR C 314 " -0.009 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 146 2.58 - 3.16: 12687 3.16 - 3.74: 19520 3.74 - 4.32: 28448 4.32 - 4.90: 46933 Nonbonded interactions: 107734 Sorted by model distance: nonbonded pdb=" OH TYR D 158 " pdb=" OE1 GLU D 195 " model vdw 2.005 2.440 nonbonded pdb=" O LEU D 193 " pdb=" OG SER D 197 " model vdw 2.013 2.440 nonbonded pdb=" OG1 THR D 14 " pdb=" O VAL D 34 " model vdw 2.068 2.440 nonbonded pdb=" OH TYR A 158 " pdb=" OE1 GLU A 195 " model vdw 2.081 2.440 nonbonded pdb=" O LEU A 193 " pdb=" OG SER A 197 " model vdw 2.096 2.440 ... (remaining 107729 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' selection = chain 'C' selection = chain 'D' } 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: 0.760 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: 3.770 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 36.510 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 0.052 13796 Z= 0.244 Angle : 0.581 7.009 18768 Z= 0.319 Chirality : 0.044 0.175 2104 Planarity : 0.004 0.040 2472 Dihedral : 12.554 111.630 5012 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 32.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.64 % Favored : 89.31 % Rotamer: Outliers : 4.34 % Allowed : 3.06 % Favored : 92.59 % 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: -4.16 (0.18), residues: 1824 helix: -1.69 (0.19), residues: 648 sheet: -4.45 (0.25), residues: 200 loop : -3.22 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.002 0.001 HIS A 409 PHE 0.007 0.001 PHE D 230 TYR 0.015 0.001 TYR D 36 ARG 0.003 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 281 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 GLN cc_start: 0.7381 (tt0) cc_final: 0.7157 (tt0) REVERT: B 172 LYS cc_start: 0.7080 (ttpt) cc_final: 0.6662 (tptt) REVERT: B 200 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.7227 (ptm160) REVERT: B 287 ASP cc_start: 0.7236 (t0) cc_final: 0.6862 (t0) REVERT: B 401 LYS cc_start: 0.8474 (mttp) cc_final: 0.8211 (mtpt) REVERT: A 260 ARG cc_start: 0.8162 (tpt-90) cc_final: 0.7484 (ttm110) REVERT: A 363 TYR cc_start: 0.8061 (m-80) cc_final: 0.7700 (m-80) REVERT: C 58 SER cc_start: 0.8274 (m) cc_final: 0.7957 (p) REVERT: C 60 GLN cc_start: 0.7385 (tt0) cc_final: 0.7172 (tt0) REVERT: C 200 ARG cc_start: 0.7823 (mtp-110) cc_final: 0.7233 (ptm160) REVERT: C 287 ASP cc_start: 0.7246 (t0) cc_final: 0.6846 (t0) REVERT: D 260 ARG cc_start: 0.8144 (tpt-90) cc_final: 0.7454 (ttm110) REVERT: D 362 GLU cc_start: 0.8026 (tt0) cc_final: 0.7693 (tt0) REVERT: D 431 ARG cc_start: 0.8496 (ttt-90) cc_final: 0.7751 (tmt-80) outliers start: 61 outliers final: 23 residues processed: 325 average time/residue: 0.2906 time to fit residues: 133.0055 Evaluate side-chains 213 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 0.0970 chunk 163 optimal weight: 0.1980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 84 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN C 84 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13796 Z= 0.193 Angle : 0.619 6.581 18768 Z= 0.312 Chirality : 0.046 0.361 2104 Planarity : 0.004 0.041 2472 Dihedral : 6.958 71.765 2043 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.49 % Allowed : 9.54 % Favored : 87.96 % 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: -3.17 (0.19), residues: 1824 helix: -1.13 (0.20), residues: 676 sheet: -3.48 (0.29), residues: 200 loop : -2.55 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.005 0.001 HIS C 6 PHE 0.012 0.001 PHE B 230 TYR 0.015 0.001 TYR B 129 ARG 0.004 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 214 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 SER cc_start: 0.8211 (m) cc_final: 0.7945 (p) REVERT: B 182 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.7987 (t) REVERT: B 200 ARG cc_start: 0.7315 (mtp-110) cc_final: 0.7079 (ptm160) REVERT: B 272 MET cc_start: 0.8613 (ttm) cc_final: 0.8393 (ttp) REVERT: B 401 LYS cc_start: 0.8484 (mttp) cc_final: 0.8172 (mtpt) REVERT: A 84 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: A 260 ARG cc_start: 0.7915 (tpt-90) cc_final: 0.7530 (tpp-160) REVERT: A 311 MET cc_start: 0.8946 (mmm) cc_final: 0.8678 (mmm) REVERT: A 363 TYR cc_start: 0.8104 (m-80) cc_final: 0.7773 (m-80) REVERT: A 452 ASP cc_start: 0.7640 (t0) cc_final: 0.7235 (t0) REVERT: C 58 SER cc_start: 0.8282 (m) cc_final: 0.7923 (p) REVERT: C 200 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.7138 (ptm160) REVERT: C 272 MET cc_start: 0.8636 (ttm) cc_final: 0.8382 (ttp) REVERT: D 18 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7909 (ttt-90) REVERT: D 35 GLU cc_start: 0.7800 (tt0) cc_final: 0.7419 (tt0) REVERT: D 147 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: D 158 TYR cc_start: 0.8139 (t80) cc_final: 0.7815 (t80) REVERT: D 185 THR cc_start: 0.7947 (m) cc_final: 0.7704 (m) REVERT: D 228 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7627 (mm-30) REVERT: D 260 ARG cc_start: 0.7905 (tpt-90) cc_final: 0.7192 (ttm110) REVERT: D 428 LYS cc_start: 0.8583 (tptm) cc_final: 0.8360 (tttt) REVERT: D 454 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7504 (mp) outliers start: 35 outliers final: 20 residues processed: 236 average time/residue: 0.2558 time to fit residues: 88.3873 Evaluate side-chains 204 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 454 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.2980 chunk 50 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 45 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN C 5 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13796 Z= 0.259 Angle : 0.618 6.947 18768 Z= 0.306 Chirality : 0.045 0.138 2104 Planarity : 0.004 0.045 2472 Dihedral : 6.114 69.090 2024 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.06 % Allowed : 13.96 % Favored : 82.98 % 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: -2.79 (0.19), residues: 1824 helix: -0.90 (0.20), residues: 660 sheet: -2.90 (0.32), residues: 200 loop : -2.33 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 310 HIS 0.007 0.002 HIS C 348 PHE 0.010 0.001 PHE A 306 TYR 0.018 0.001 TYR D 36 ARG 0.003 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 179 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 SER cc_start: 0.8296 (m) cc_final: 0.7994 (p) REVERT: B 152 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7390 (mt-10) REVERT: B 182 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8357 (t) REVERT: B 200 ARG cc_start: 0.7358 (mtp-110) cc_final: 0.7097 (ptm160) REVERT: B 401 LYS cc_start: 0.8512 (mttp) cc_final: 0.8194 (mtpt) REVERT: B 436 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8070 (pp) REVERT: A 228 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 260 ARG cc_start: 0.7943 (tpt-90) cc_final: 0.7371 (ttm110) REVERT: A 311 MET cc_start: 0.8936 (mmm) cc_final: 0.8648 (mmm) REVERT: A 363 TYR cc_start: 0.8163 (m-80) cc_final: 0.7819 (m-80) REVERT: A 404 ASP cc_start: 0.7644 (m-30) cc_final: 0.7442 (m-30) REVERT: A 452 ASP cc_start: 0.7529 (t0) cc_final: 0.7141 (t0) REVERT: C 58 SER cc_start: 0.8246 (m) cc_final: 0.7853 (p) REVERT: C 152 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7495 (mt-10) REVERT: C 200 ARG cc_start: 0.7419 (mtp-110) cc_final: 0.7141 (ptm160) REVERT: C 311 MET cc_start: 0.9321 (mmp) cc_final: 0.9051 (mmm) REVERT: D 35 GLU cc_start: 0.7955 (tt0) cc_final: 0.7666 (tt0) REVERT: D 74 ASN cc_start: 0.7379 (t0) cc_final: 0.7155 (t0) REVERT: D 147 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: D 185 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7992 (m) REVERT: D 228 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7759 (mm-30) REVERT: D 260 ARG cc_start: 0.7901 (tpt-90) cc_final: 0.7219 (ttm110) REVERT: D 428 LYS cc_start: 0.8583 (tptm) cc_final: 0.8299 (tttt) outliers start: 43 outliers final: 25 residues processed: 211 average time/residue: 0.2604 time to fit residues: 80.4168 Evaluate side-chains 194 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 84 GLN A 123 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN D 123 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 13796 Z= 0.590 Angle : 0.804 8.446 18768 Z= 0.402 Chirality : 0.052 0.150 2104 Planarity : 0.006 0.052 2472 Dihedral : 6.568 62.249 2020 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 3.85 % Allowed : 15.67 % Favored : 80.48 % 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: -2.95 (0.19), residues: 1824 helix: -1.28 (0.19), residues: 664 sheet: -2.76 (0.33), residues: 204 loop : -2.29 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 310 HIS 0.012 0.003 HIS A 348 PHE 0.010 0.002 PHE C 252 TYR 0.028 0.002 TYR A 128 ARG 0.005 0.001 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 155 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: B 58 SER cc_start: 0.8439 (m) cc_final: 0.8018 (p) REVERT: A 35 GLU cc_start: 0.8174 (tt0) cc_final: 0.7968 (tt0) REVERT: A 228 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 363 TYR cc_start: 0.8264 (m-80) cc_final: 0.8008 (m-80) REVERT: A 404 ASP cc_start: 0.7790 (m-30) cc_final: 0.7233 (m-30) REVERT: A 431 ARG cc_start: 0.8011 (ttt-90) cc_final: 0.7581 (tmt-80) REVERT: C 311 MET cc_start: 0.9370 (mmp) cc_final: 0.8730 (mmm) REVERT: D 18 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8201 (ttt-90) REVERT: D 74 ASN cc_start: 0.7651 (t0) cc_final: 0.7376 (t0) REVERT: D 147 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8366 (pm20) REVERT: D 158 TYR cc_start: 0.8355 (t80) cc_final: 0.8038 (t80) REVERT: D 228 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7858 (mm-30) REVERT: D 260 ARG cc_start: 0.8102 (tpt-90) cc_final: 0.7291 (ttm110) REVERT: D 296 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: D 404 ASP cc_start: 0.7789 (m-30) cc_final: 0.7325 (m-30) outliers start: 54 outliers final: 34 residues processed: 194 average time/residue: 0.2312 time to fit residues: 67.8008 Evaluate side-chains 182 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 0.0980 chunk 129 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 84 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.003 0.047 13796 Z= 0.175 Angle : 0.584 6.800 18768 Z= 0.290 Chirality : 0.044 0.179 2104 Planarity : 0.004 0.040 2472 Dihedral : 5.777 68.709 2019 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.13 % Allowed : 17.95 % Favored : 78.92 % 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: -2.43 (0.19), residues: 1824 helix: -0.83 (0.20), residues: 668 sheet: -2.36 (0.34), residues: 204 loop : -2.02 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 310 HIS 0.006 0.001 HIS C 6 PHE 0.007 0.001 PHE C 252 TYR 0.016 0.001 TYR B 36 ARG 0.008 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 174 time to evaluate : 1.530 Fit side-chains revert: symmetry clash REVERT: B 58 SER cc_start: 0.8287 (m) cc_final: 0.7989 (p) REVERT: B 152 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7416 (mt-10) REVERT: B 200 ARG cc_start: 0.7373 (mtp-110) cc_final: 0.6918 (ptm160) REVERT: B 401 LYS cc_start: 0.8551 (mttp) cc_final: 0.8195 (mtpt) REVERT: B 436 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8098 (pp) REVERT: A 228 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 363 TYR cc_start: 0.8209 (m-80) cc_final: 0.7932 (m-80) REVERT: A 404 ASP cc_start: 0.7719 (m-30) cc_final: 0.7245 (m-30) REVERT: A 452 ASP cc_start: 0.7359 (t0) cc_final: 0.6941 (t0) REVERT: C 58 SER cc_start: 0.8236 (m) cc_final: 0.7837 (p) REVERT: C 152 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7598 (mt-10) REVERT: C 200 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.7140 (ptm160) REVERT: C 311 MET cc_start: 0.9241 (mmp) cc_final: 0.9034 (mmm) REVERT: C 436 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8165 (pp) REVERT: D 18 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7943 (ttt-90) REVERT: D 84 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8431 (pt0) REVERT: D 147 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: D 228 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7716 (mm-30) REVERT: D 260 ARG cc_start: 0.8008 (tpt-90) cc_final: 0.7178 (ttm110) REVERT: D 296 ASP cc_start: 0.8456 (t0) cc_final: 0.8052 (m-30) REVERT: D 404 ASP cc_start: 0.7617 (m-30) cc_final: 0.7206 (m-30) REVERT: D 428 LYS cc_start: 0.8643 (tptm) cc_final: 0.8354 (tttt) outliers start: 44 outliers final: 28 residues processed: 213 average time/residue: 0.2380 time to fit residues: 75.8809 Evaluate side-chains 190 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 174 optimal weight: 0.0970 chunk 144 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13796 Z= 0.221 Angle : 0.590 6.740 18768 Z= 0.291 Chirality : 0.045 0.163 2104 Planarity : 0.004 0.042 2472 Dihedral : 5.550 69.995 2018 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.92 % Allowed : 17.31 % Favored : 78.77 % 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: -2.20 (0.20), residues: 1824 helix: -0.71 (0.20), residues: 668 sheet: -2.08 (0.35), residues: 204 loop : -1.86 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 310 HIS 0.006 0.001 HIS C 348 PHE 0.008 0.001 PHE D 306 TYR 0.015 0.001 TYR B 36 ARG 0.005 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 165 time to evaluate : 1.488 Fit side-chains revert: symmetry clash REVERT: B 58 SER cc_start: 0.8285 (m) cc_final: 0.7966 (p) REVERT: B 200 ARG cc_start: 0.7426 (mtp-110) cc_final: 0.6955 (ptm160) REVERT: B 401 LYS cc_start: 0.8544 (mttp) cc_final: 0.8188 (mtpt) REVERT: B 436 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8126 (pp) REVERT: A 84 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: A 228 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 260 ARG cc_start: 0.8282 (tpp80) cc_final: 0.7533 (ttm110) REVERT: A 296 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: A 363 TYR cc_start: 0.8230 (m-80) cc_final: 0.7946 (m-80) REVERT: A 404 ASP cc_start: 0.7743 (m-30) cc_final: 0.7280 (m-30) REVERT: A 431 ARG cc_start: 0.8035 (ttt-90) cc_final: 0.7598 (tmt-80) REVERT: A 451 TYR cc_start: 0.8301 (t80) cc_final: 0.8042 (t80) REVERT: A 452 ASP cc_start: 0.7407 (t0) cc_final: 0.6964 (t0) REVERT: C 58 SER cc_start: 0.8216 (m) cc_final: 0.7842 (p) REVERT: C 152 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7616 (mt-10) REVERT: C 200 ARG cc_start: 0.7475 (mtp-110) cc_final: 0.7092 (ptm160) REVERT: C 436 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8079 (pp) REVERT: D 18 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7965 (ttt-90) REVERT: D 84 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: D 147 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: D 228 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7711 (mm-30) REVERT: D 260 ARG cc_start: 0.8051 (tpt-90) cc_final: 0.7238 (ttm110) REVERT: D 296 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: D 404 ASP cc_start: 0.7694 (m-30) cc_final: 0.7299 (m-30) REVERT: D 428 LYS cc_start: 0.8640 (tptm) cc_final: 0.8337 (tttt) outliers start: 55 outliers final: 37 residues processed: 210 average time/residue: 0.2383 time to fit residues: 74.5104 Evaluate side-chains 204 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 0.2980 chunk 97 optimal weight: 0.3980 chunk 173 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 84 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13796 Z= 0.190 Angle : 0.576 7.930 18768 Z= 0.283 Chirality : 0.044 0.139 2104 Planarity : 0.004 0.040 2472 Dihedral : 5.359 70.209 2018 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.56 % Allowed : 18.30 % Favored : 78.13 % 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: -1.99 (0.20), residues: 1824 helix: -0.59 (0.21), residues: 668 sheet: -1.81 (0.36), residues: 204 loop : -1.74 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 310 HIS 0.005 0.001 HIS C 348 PHE 0.006 0.001 PHE D 306 TYR 0.015 0.001 TYR D 451 ARG 0.006 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 165 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: B 58 SER cc_start: 0.8262 (m) cc_final: 0.8040 (p) REVERT: B 200 ARG cc_start: 0.7339 (mtp-110) cc_final: 0.6903 (ptm160) REVERT: B 287 ASP cc_start: 0.7200 (t0) cc_final: 0.6913 (t0) REVERT: B 401 LYS cc_start: 0.8535 (mttp) cc_final: 0.8170 (mtpt) REVERT: B 436 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8107 (pp) REVERT: A 84 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: A 228 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7597 (mm-30) REVERT: A 254 MET cc_start: 0.8537 (tpp) cc_final: 0.8333 (tpt) REVERT: A 260 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7537 (ttm110) REVERT: A 296 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: A 363 TYR cc_start: 0.8211 (m-80) cc_final: 0.7914 (m-80) REVERT: A 404 ASP cc_start: 0.7751 (m-30) cc_final: 0.7248 (m-30) REVERT: A 431 ARG cc_start: 0.8029 (ttt-90) cc_final: 0.7603 (tmt-80) REVERT: A 451 TYR cc_start: 0.8252 (t80) cc_final: 0.7983 (t80) REVERT: A 452 ASP cc_start: 0.7396 (t0) cc_final: 0.6922 (t0) REVERT: C 9 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7326 (mp0) REVERT: C 58 SER cc_start: 0.8119 (m) cc_final: 0.7796 (p) REVERT: C 152 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7610 (mt-10) REVERT: C 200 ARG cc_start: 0.7379 (mtp-110) cc_final: 0.7047 (ptm160) REVERT: C 436 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8074 (pp) REVERT: D 18 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7958 (ttt-90) REVERT: D 84 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: D 147 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: D 228 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7683 (mm-30) REVERT: D 296 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: D 404 ASP cc_start: 0.7697 (m-30) cc_final: 0.7320 (m-30) REVERT: D 428 LYS cc_start: 0.8685 (tptm) cc_final: 0.8406 (tttt) outliers start: 50 outliers final: 34 residues processed: 207 average time/residue: 0.2397 time to fit residues: 74.2305 Evaluate side-chains 195 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 136 optimal weight: 0.6980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13796 Z= 0.258 Angle : 0.606 7.261 18768 Z= 0.297 Chirality : 0.045 0.156 2104 Planarity : 0.004 0.043 2472 Dihedral : 5.281 67.131 2017 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.20 % Allowed : 18.16 % Favored : 77.64 % 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: -1.92 (0.20), residues: 1824 helix: -0.54 (0.21), residues: 660 sheet: -2.03 (0.35), residues: 196 loop : -1.62 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 310 HIS 0.006 0.001 HIS C 348 PHE 0.007 0.001 PHE D 306 TYR 0.016 0.001 TYR D 36 ARG 0.004 0.000 ARG D 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 152 time to evaluate : 1.505 Fit side-chains revert: symmetry clash REVERT: B 58 SER cc_start: 0.8264 (m) cc_final: 0.8014 (p) REVERT: B 84 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8426 (pt0) REVERT: B 200 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.6930 (ptm160) REVERT: B 287 ASP cc_start: 0.7260 (t0) cc_final: 0.6980 (t0) REVERT: B 374 GLU cc_start: 0.5598 (OUTLIER) cc_final: 0.4949 (tt0) REVERT: B 401 LYS cc_start: 0.8545 (mttp) cc_final: 0.8175 (mtpt) REVERT: B 436 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8127 (pp) REVERT: A 84 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: A 228 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7770 (mm-30) REVERT: A 254 MET cc_start: 0.8528 (tpp) cc_final: 0.8320 (tpt) REVERT: A 296 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: A 363 TYR cc_start: 0.8227 (m-80) cc_final: 0.7934 (m-80) REVERT: A 404 ASP cc_start: 0.7763 (m-30) cc_final: 0.7309 (m-30) REVERT: A 431 ARG cc_start: 0.8038 (ttt-90) cc_final: 0.7630 (tmt-80) REVERT: A 451 TYR cc_start: 0.8250 (t80) cc_final: 0.7979 (t80) REVERT: A 452 ASP cc_start: 0.7423 (t0) cc_final: 0.6988 (t0) REVERT: C 9 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7357 (mp0) REVERT: C 58 SER cc_start: 0.8033 (m) cc_final: 0.7682 (p) REVERT: C 152 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7597 (mt-10) REVERT: C 200 ARG cc_start: 0.7422 (mtp-110) cc_final: 0.7045 (ptm160) REVERT: C 436 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8120 (pp) REVERT: D 18 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7961 (ttt-90) REVERT: D 84 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: D 147 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8068 (pm20) REVERT: D 228 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7699 (mm-30) REVERT: D 296 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: D 368 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8321 (ptm) REVERT: D 388 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8528 (tp30) REVERT: D 404 ASP cc_start: 0.7732 (m-30) cc_final: 0.7335 (m-30) REVERT: D 428 LYS cc_start: 0.8699 (tptm) cc_final: 0.8422 (tttt) outliers start: 59 outliers final: 40 residues processed: 200 average time/residue: 0.2269 time to fit residues: 69.0004 Evaluate side-chains 201 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 150 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 152 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN A 6 HIS ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13796 Z= 0.173 Angle : 0.569 7.147 18768 Z= 0.278 Chirality : 0.044 0.140 2104 Planarity : 0.004 0.039 2472 Dihedral : 4.991 69.813 2015 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.56 % Allowed : 19.02 % Favored : 77.42 % 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: -1.72 (0.20), residues: 1824 helix: -0.41 (0.21), residues: 668 sheet: -1.78 (0.35), residues: 196 loop : -1.51 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 310 HIS 0.005 0.001 HIS C 348 PHE 0.006 0.001 PHE D 316 TYR 0.016 0.001 TYR D 451 ARG 0.004 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 164 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: B 200 ARG cc_start: 0.7278 (mtp-110) cc_final: 0.6842 (ptm160) REVERT: B 287 ASP cc_start: 0.7215 (t0) cc_final: 0.6978 (t0) REVERT: B 401 LYS cc_start: 0.8522 (mttp) cc_final: 0.8158 (mtpt) REVERT: B 436 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8114 (pp) REVERT: A 84 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8137 (pt0) REVERT: A 228 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 254 MET cc_start: 0.8559 (tpp) cc_final: 0.8352 (tpt) REVERT: A 260 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7631 (ttm110) REVERT: A 296 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: A 363 TYR cc_start: 0.8182 (m-80) cc_final: 0.7881 (m-80) REVERT: A 404 ASP cc_start: 0.7801 (m-30) cc_final: 0.7336 (m-30) REVERT: A 431 ARG cc_start: 0.8020 (ttt-90) cc_final: 0.7623 (tmt-80) REVERT: A 451 TYR cc_start: 0.8184 (t80) cc_final: 0.7900 (t80) REVERT: A 452 ASP cc_start: 0.7401 (t0) cc_final: 0.6931 (t0) REVERT: C 9 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7273 (mp0) REVERT: C 58 SER cc_start: 0.8134 (m) cc_final: 0.7872 (p) REVERT: C 200 ARG cc_start: 0.7302 (mtp-110) cc_final: 0.6979 (ptm160) REVERT: C 287 ASP cc_start: 0.6963 (t0) cc_final: 0.6702 (t0) REVERT: C 436 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8091 (pp) REVERT: D 18 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7808 (ttt-90) REVERT: D 84 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8245 (pt0) REVERT: D 147 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8019 (pm20) REVERT: D 228 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7611 (mm-30) REVERT: D 296 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: D 368 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8186 (ptm) REVERT: D 388 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8452 (tp30) REVERT: D 404 ASP cc_start: 0.7765 (m-30) cc_final: 0.7551 (m-30) REVERT: D 428 LYS cc_start: 0.8738 (tptm) cc_final: 0.8422 (tttt) REVERT: D 440 GLU cc_start: 0.5786 (tm-30) cc_final: 0.5526 (tm-30) outliers start: 50 outliers final: 37 residues processed: 206 average time/residue: 0.2350 time to fit residues: 73.2931 Evaluate side-chains 200 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 154 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN A 84 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.003 0.041 13796 Z= 0.212 Angle : 0.586 6.659 18768 Z= 0.286 Chirality : 0.045 0.140 2104 Planarity : 0.004 0.041 2472 Dihedral : 4.963 68.344 2015 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.21 % Allowed : 19.37 % Favored : 77.42 % 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: -1.64 (0.20), residues: 1824 helix: -0.37 (0.21), residues: 668 sheet: -1.59 (0.36), residues: 196 loop : -1.47 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.006 0.001 HIS B 6 PHE 0.008 0.001 PHE D 306 TYR 0.013 0.001 TYR D 36 ARG 0.004 0.000 ARG B 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 156 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: B 200 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.6870 (ptm160) REVERT: B 287 ASP cc_start: 0.7271 (t0) cc_final: 0.7064 (t0) REVERT: B 401 LYS cc_start: 0.8552 (mttp) cc_final: 0.8172 (mtpt) REVERT: B 436 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8160 (pp) REVERT: A 84 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7987 (pt0) REVERT: A 228 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 254 MET cc_start: 0.8566 (tpp) cc_final: 0.8355 (tpt) REVERT: A 260 ARG cc_start: 0.8365 (tpp80) cc_final: 0.7786 (ttm110) REVERT: A 296 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: A 363 TYR cc_start: 0.8211 (m-80) cc_final: 0.7943 (m-80) REVERT: A 404 ASP cc_start: 0.7802 (m-30) cc_final: 0.7375 (m-30) REVERT: A 431 ARG cc_start: 0.8025 (ttt-90) cc_final: 0.7646 (tmt-80) REVERT: A 451 TYR cc_start: 0.8197 (t80) cc_final: 0.7919 (t80) REVERT: A 452 ASP cc_start: 0.7422 (t0) cc_final: 0.6939 (t0) REVERT: C 9 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7286 (mp0) REVERT: C 200 ARG cc_start: 0.7307 (mtp-110) cc_final: 0.6975 (ptm160) REVERT: C 436 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8166 (pp) REVERT: D 18 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7948 (ttt-90) REVERT: D 84 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8302 (pt0) REVERT: D 147 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: D 228 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7610 (mm-30) REVERT: D 296 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: D 368 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8203 (ptm) REVERT: D 388 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8427 (tp30) REVERT: D 404 ASP cc_start: 0.7773 (m-30) cc_final: 0.7565 (m-30) REVERT: D 428 LYS cc_start: 0.8723 (tptm) cc_final: 0.8411 (tttt) outliers start: 45 outliers final: 34 residues processed: 194 average time/residue: 0.2343 time to fit residues: 68.6423 Evaluate side-chains 194 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 6.9990 chunk 43 optimal weight: 0.0870 chunk 131 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN A 84 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.135160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.111364 restraints weight = 16876.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.113957 restraints weight = 11504.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.115781 restraints weight = 8878.929| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13796 Z= 0.191 Angle : 0.575 6.740 18768 Z= 0.280 Chirality : 0.044 0.139 2104 Planarity : 0.004 0.040 2472 Dihedral : 4.909 69.289 2015 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.49 % Allowed : 19.37 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1824 helix: -0.28 (0.21), residues: 664 sheet: -1.42 (0.36), residues: 196 loop : -1.44 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 310 HIS 0.005 0.001 HIS C 6 PHE 0.009 0.001 PHE A 306 TYR 0.016 0.001 TYR D 451 ARG 0.004 0.000 ARG D 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2631.69 seconds wall clock time: 49 minutes 2.26 seconds (2942.26 seconds total)