Starting phenix.real_space_refine on Sat Mar 16 13:21:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/03_2024/7to3_26028_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/03_2024/7to3_26028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/03_2024/7to3_26028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/03_2024/7to3_26028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/03_2024/7to3_26028_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/03_2024/7to3_26028_updated.pdb" } resolution = 2.74 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= 0.010 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 44 5.16 5 C 9346 2.51 5 N 2572 2.21 5 O 2786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14764 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4421 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 533} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4421 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 533} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2878 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2878 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 83 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 83 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 8.00, per 1000 atoms: 0.54 Number of scatterers: 14764 At special positions: 0 Unit cell: (147, 126.84, 110.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 12 15.00 Mg 4 11.99 O 2786 8.00 N 2572 7.00 C 9346 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.22 Conformation dependent library (CDL) restraints added in 2.7 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 10 sheets defined 34.5% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 119 through 122 No H-bonds generated for 'chain 'A' and resid 119 through 122' Processing helix chain 'A' and resid 129 through 148 Processing helix chain 'A' and resid 179 through 188 Proline residue: A 183 - end of helix removed outlier: 4.243A pdb=" N SER A 187 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 272 through 285 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 374 through 377 No H-bonds generated for 'chain 'A' and resid 374 through 377' Processing helix chain 'A' and resid 388 through 400 removed outlier: 3.575A pdb=" N MET A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.678A pdb=" N GLN A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 557 through 576 Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 129 through 148 Processing helix chain 'B' and resid 179 through 188 Proline residue: B 183 - end of helix removed outlier: 4.243A pdb=" N SER B 187 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 230 No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 272 through 285 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 374 through 377 No H-bonds generated for 'chain 'B' and resid 374 through 377' Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.574A pdb=" N MET B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 432 through 441 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.676A pdb=" N GLN B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 521 through 530 Processing helix chain 'B' and resid 557 through 576 Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 18 through 37 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 85 through 99 removed outlier: 4.234A pdb=" N PHE C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE C 93 " --> pdb=" O MET C 89 " (cutoff:3.500A) Proline residue: C 94 - end of helix Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 207 through 220 Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 310 through 332 removed outlier: 3.556A pdb=" N ALA C 332 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 347 removed outlier: 3.960A pdb=" N LEU C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 13 Processing helix chain 'D' and resid 18 through 37 Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 85 through 99 removed outlier: 4.234A pdb=" N PHE D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) Proline residue: D 94 - end of helix Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 207 through 220 Processing helix chain 'D' and resid 225 through 238 Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 267 through 281 Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 310 through 332 removed outlier: 3.556A pdb=" N ALA D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 347 removed outlier: 3.961A pdb=" N LEU D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 45 Processing sheet with id= B, first strand: chain 'A' and resid 357 through 360 removed outlier: 6.965A pdb=" N SER A 196 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE A 212 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 194 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER A 197 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR A 236 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 294 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER A 241 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 296 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A 311 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 593 through 597 removed outlier: 6.861A pdb=" N SER A 448 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N ILE A 407 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG A 450 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 39 through 45 Processing sheet with id= E, first strand: chain 'B' and resid 357 through 360 removed outlier: 6.964A pdb=" N SER B 196 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE B 212 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE B 194 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 197 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR B 236 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 294 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N SER B 241 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 296 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 311 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 593 through 597 removed outlier: 6.861A pdb=" N SER B 448 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ILE B 407 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG B 450 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 104 through 107 removed outlier: 7.217A pdb=" N ASP C 121 " --> pdb=" O PRO C 68 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL C 70 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 123 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 72 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR C 125 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 74 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP C 71 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 125 through 127 Processing sheet with id= I, first strand: chain 'D' and resid 104 through 107 removed outlier: 7.217A pdb=" N ASP D 121 " --> pdb=" O PRO D 68 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 70 " --> pdb=" O ASP D 121 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL D 123 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE D 72 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR D 125 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 74 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP D 71 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 125 through 127 540 hydrogen bonds defined for protein. 1548 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: 4.71 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4847 1.35 - 1.46: 3467 1.46 - 1.58: 6746 1.58 - 1.69: 18 1.69 - 1.81: 72 Bond restraints: 15150 Sorted by residual: bond pdb=" CA TRP D 24 " pdb=" CB TRP D 24 " ideal model delta sigma weight residual 1.528 1.549 -0.021 1.59e-02 3.96e+03 1.75e+00 bond pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " ideal model delta sigma weight residual 1.528 1.549 -0.021 1.59e-02 3.96e+03 1.68e+00 bond pdb=" C GLU B 69 " pdb=" O GLU B 69 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.24e-02 6.50e+03 9.88e-01 bond pdb=" C4 ADP D 405 " pdb=" C5 ADP D 405 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.57e-01 bond pdb=" C4 AMP D 401 " pdb=" C5 AMP D 401 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.50e-01 ... (remaining 15145 not shown) Histogram of bond angle deviations from ideal: 98.35 - 106.67: 611 106.67 - 114.98: 9053 114.98 - 123.30: 10172 123.30 - 131.61: 738 131.61 - 139.93: 80 Bond angle restraints: 20654 Sorted by residual: angle pdb=" N ILE B 220 " pdb=" CA ILE B 220 " pdb=" C ILE B 220 " ideal model delta sigma weight residual 113.71 110.28 3.43 9.50e-01 1.11e+00 1.31e+01 angle pdb=" N ILE A 220 " pdb=" CA ILE A 220 " pdb=" C ILE A 220 " ideal model delta sigma weight residual 113.71 110.29 3.42 9.50e-01 1.11e+00 1.30e+01 angle pdb=" N TRP C 24 " pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " ideal model delta sigma weight residual 110.16 115.00 -4.84 1.48e+00 4.57e-01 1.07e+01 angle pdb=" N TRP D 24 " pdb=" CA TRP D 24 " pdb=" CB TRP D 24 " ideal model delta sigma weight residual 110.16 114.93 -4.77 1.48e+00 4.57e-01 1.04e+01 angle pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " pdb=" CG TRP C 24 " ideal model delta sigma weight residual 113.60 119.55 -5.95 1.90e+00 2.77e-01 9.81e+00 ... (remaining 20649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.13: 8900 34.13 - 68.26: 124 68.26 - 102.39: 2 102.39 - 136.51: 2 136.51 - 170.64: 4 Dihedral angle restraints: 9032 sinusoidal: 3670 harmonic: 5362 Sorted by residual: dihedral pdb=" O2A ADP D 405 " pdb=" O3A ADP D 405 " pdb=" PA ADP D 405 " pdb=" PB ADP D 405 " ideal model delta sinusoidal sigma weight residual 300.00 129.36 170.64 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP C 405 " pdb=" O3A ADP C 405 " pdb=" PA ADP C 405 " pdb=" PB ADP C 405 " ideal model delta sinusoidal sigma weight residual 300.00 129.37 170.63 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' AMP C 401 " pdb=" O5' AMP C 401 " pdb=" P AMP C 401 " pdb=" O3P AMP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 148.68 151.32 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 9029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1643 0.033 - 0.067: 426 0.067 - 0.100: 119 0.100 - 0.133: 54 0.133 - 0.167: 8 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE B 74 " pdb=" N ILE B 74 " pdb=" C ILE B 74 " pdb=" CB ILE B 74 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 2247 not shown) Planarity restraints: 2648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 24 " -0.034 2.00e-02 2.50e+03 3.68e-02 3.38e+01 pdb=" CG TRP D 24 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TRP D 24 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP D 24 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 24 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP D 24 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 24 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 24 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 24 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 24 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 24 " 0.034 2.00e-02 2.50e+03 3.67e-02 3.36e+01 pdb=" CG TRP C 24 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP C 24 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP C 24 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 24 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 24 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 24 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 24 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 24 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 24 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 49 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 50 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " 0.027 5.00e-02 4.00e+02 ... (remaining 2645 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 34 2.63 - 3.20: 12092 3.20 - 3.76: 22085 3.76 - 4.33: 31875 4.33 - 4.90: 51731 Nonbonded interactions: 117817 Sorted by model distance: nonbonded pdb="MG MG C 403 " pdb=" O2B ATP C 404 " model vdw 2.062 2.170 nonbonded pdb="MG MG D 403 " pdb=" O2B ATP D 404 " model vdw 2.062 2.170 nonbonded pdb=" OD2 ASP C 69 " pdb="MG MG C 402 " model vdw 2.079 2.170 nonbonded pdb=" OD2 ASP D 69 " pdb="MG MG D 402 " model vdw 2.080 2.170 nonbonded pdb=" O ALA C 132 " pdb=" ND1 HIS C 136 " model vdw 2.317 2.520 ... (remaining 117812 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' } ncs_group { reference = 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 individual isotropic 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: 5.670 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: 0.020 Extract box with map and model: 18.220 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 40.020 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.002 0.023 15150 Z= 0.132 Angle : 0.544 5.950 20654 Z= 0.281 Chirality : 0.037 0.167 2250 Planarity : 0.004 0.049 2648 Dihedral : 12.122 170.644 5540 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1830 helix: 2.69 (0.20), residues: 664 sheet: 0.57 (0.27), residues: 348 loop : -1.32 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.001 TRP D 24 HIS 0.005 0.001 HIS D 206 PHE 0.011 0.001 PHE A 510 TYR 0.009 0.001 TYR D 225 ARG 0.001 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8130 (mt0) cc_final: 0.7499 (mm-40) REVERT: B 37 LYS cc_start: 0.9103 (mttt) cc_final: 0.8877 (tmmm) REVERT: B 39 TRP cc_start: 0.7299 (m100) cc_final: 0.6744 (m100) REVERT: B 414 GLN cc_start: 0.8084 (mt0) cc_final: 0.7459 (mm-40) REVERT: C 90 ASP cc_start: 0.8213 (m-30) cc_final: 0.8006 (m-30) REVERT: C 242 ASP cc_start: 0.8406 (m-30) cc_final: 0.7928 (t0) REVERT: D 242 ASP cc_start: 0.8403 (m-30) cc_final: 0.7938 (t0) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 1.5732 time to fit residues: 443.1692 Evaluate side-chains 110 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.0670 chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN B 94 ASN C 8 ASN C 210 GLN C 254 HIS D 8 ASN D 210 GLN D 254 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15150 Z= 0.194 Angle : 0.554 6.179 20654 Z= 0.262 Chirality : 0.039 0.179 2250 Planarity : 0.004 0.058 2648 Dihedral : 9.523 141.170 2088 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.68 % Allowed : 7.56 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1830 helix: 2.49 (0.20), residues: 660 sheet: 0.64 (0.27), residues: 334 loop : -1.06 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 24 HIS 0.008 0.001 HIS C 206 PHE 0.014 0.001 PHE B 510 TYR 0.015 0.001 TYR D 286 ARG 0.008 0.000 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.7566 (m100) cc_final: 0.6808 (m100) REVERT: A 215 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7353 (m-40) REVERT: A 414 GLN cc_start: 0.8214 (mt0) cc_final: 0.7497 (mm-40) REVERT: B 37 LYS cc_start: 0.9132 (mttt) cc_final: 0.8898 (tmmm) REVERT: B 39 TRP cc_start: 0.7423 (m100) cc_final: 0.6765 (m100) REVERT: B 215 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7375 (m-40) REVERT: B 414 GLN cc_start: 0.8195 (mt0) cc_final: 0.7472 (mm-40) REVERT: C 90 ASP cc_start: 0.8271 (m-30) cc_final: 0.8043 (m-30) REVERT: C 162 LYS cc_start: 0.8870 (pttt) cc_final: 0.8197 (tppt) REVERT: C 242 ASP cc_start: 0.8429 (m-30) cc_final: 0.7883 (t0) REVERT: D 90 ASP cc_start: 0.8308 (m-30) cc_final: 0.8034 (m-30) REVERT: D 162 LYS cc_start: 0.8797 (pttt) cc_final: 0.8214 (tppt) REVERT: D 242 ASP cc_start: 0.8401 (m-30) cc_final: 0.7864 (t0) outliers start: 26 outliers final: 12 residues processed: 133 average time/residue: 1.4098 time to fit residues: 205.5889 Evaluate side-chains 95 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 194 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 0.0050 chunk 164 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN C 254 HIS D 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15150 Z= 0.221 Angle : 0.556 7.052 20654 Z= 0.264 Chirality : 0.040 0.171 2250 Planarity : 0.004 0.046 2648 Dihedral : 8.488 120.422 2088 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.87 % Allowed : 8.46 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1830 helix: 2.40 (0.21), residues: 664 sheet: 0.80 (0.27), residues: 358 loop : -1.21 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 24 HIS 0.008 0.001 HIS D 206 PHE 0.014 0.002 PHE A 510 TYR 0.019 0.002 TYR D 286 ARG 0.007 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7415 (m-40) REVERT: A 414 GLN cc_start: 0.8251 (mt0) cc_final: 0.7447 (mm-40) REVERT: B 37 LYS cc_start: 0.9148 (mttt) cc_final: 0.8889 (tmmm) REVERT: B 215 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7428 (m-40) REVERT: B 414 GLN cc_start: 0.8212 (mt0) cc_final: 0.7448 (mm-40) REVERT: C 90 ASP cc_start: 0.8250 (m-30) cc_final: 0.8003 (m-30) REVERT: C 162 LYS cc_start: 0.8833 (pttt) cc_final: 0.8202 (tppt) REVERT: C 242 ASP cc_start: 0.8471 (m-30) cc_final: 0.7820 (t0) REVERT: C 245 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8604 (tptp) REVERT: D 90 ASP cc_start: 0.8289 (m-30) cc_final: 0.7932 (m-30) REVERT: D 162 LYS cc_start: 0.8761 (pttt) cc_final: 0.8227 (tppt) REVERT: D 242 ASP cc_start: 0.8454 (m-30) cc_final: 0.7790 (t0) outliers start: 29 outliers final: 10 residues processed: 116 average time/residue: 1.3462 time to fit residues: 172.1680 Evaluate side-chains 92 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain D residue 194 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.1980 chunk 124 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 166 optimal weight: 0.4980 chunk 175 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15150 Z= 0.166 Angle : 0.523 6.552 20654 Z= 0.245 Chirality : 0.039 0.171 2250 Planarity : 0.004 0.040 2648 Dihedral : 7.789 96.932 2088 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.68 % Allowed : 9.75 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1830 helix: 2.21 (0.21), residues: 688 sheet: 1.01 (0.27), residues: 344 loop : -1.18 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 24 HIS 0.005 0.001 HIS C 206 PHE 0.013 0.001 PHE B 510 TYR 0.016 0.001 TYR D 286 ARG 0.011 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7432 (m-40) REVERT: A 414 GLN cc_start: 0.8209 (mt0) cc_final: 0.7418 (mm-40) REVERT: B 215 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7431 (m-40) REVERT: B 414 GLN cc_start: 0.8189 (mt0) cc_final: 0.7412 (mm-40) REVERT: C 90 ASP cc_start: 0.8230 (m-30) cc_final: 0.7943 (m-30) REVERT: C 162 LYS cc_start: 0.8825 (pttt) cc_final: 0.8247 (tppt) REVERT: C 242 ASP cc_start: 0.8463 (m-30) cc_final: 0.7792 (t0) REVERT: C 245 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8585 (tptp) REVERT: D 90 ASP cc_start: 0.8292 (m-30) cc_final: 0.7946 (m-30) REVERT: D 162 LYS cc_start: 0.8751 (pttt) cc_final: 0.8291 (tppt) REVERT: D 242 ASP cc_start: 0.8435 (m-30) cc_final: 0.7774 (t0) REVERT: D 305 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8436 (mpt) outliers start: 26 outliers final: 11 residues processed: 106 average time/residue: 1.3175 time to fit residues: 154.5193 Evaluate side-chains 90 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 121 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 67 GLN B 417 ASN B 550 HIS ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15150 Z= 0.238 Angle : 0.554 6.921 20654 Z= 0.263 Chirality : 0.040 0.166 2250 Planarity : 0.004 0.039 2648 Dihedral : 7.584 78.865 2088 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.81 % Allowed : 9.88 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1830 helix: 2.08 (0.21), residues: 688 sheet: 0.94 (0.27), residues: 344 loop : -1.21 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 24 HIS 0.007 0.001 HIS C 206 PHE 0.015 0.002 PHE A 510 TYR 0.019 0.002 TYR C 286 ARG 0.007 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 78 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8741 (mtpt) REVERT: A 414 GLN cc_start: 0.8209 (mt0) cc_final: 0.7402 (mm-40) REVERT: B 380 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8738 (mtpt) REVERT: B 414 GLN cc_start: 0.8205 (mt0) cc_final: 0.7429 (mm-40) REVERT: C 90 ASP cc_start: 0.8227 (m-30) cc_final: 0.7937 (m-30) REVERT: C 162 LYS cc_start: 0.8784 (pttt) cc_final: 0.8224 (tppt) REVERT: C 242 ASP cc_start: 0.8509 (m-30) cc_final: 0.7809 (t0) REVERT: C 305 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8387 (mpt) REVERT: D 90 ASP cc_start: 0.8285 (m-30) cc_final: 0.7913 (m-30) REVERT: D 139 GLN cc_start: 0.8808 (tt0) cc_final: 0.8546 (mp10) REVERT: D 162 LYS cc_start: 0.8736 (pttt) cc_final: 0.8291 (tppt) REVERT: D 242 ASP cc_start: 0.8503 (m-30) cc_final: 0.7791 (t0) REVERT: D 305 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8194 (mpt) outliers start: 28 outliers final: 18 residues processed: 103 average time/residue: 1.3400 time to fit residues: 152.7192 Evaluate side-chains 98 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 24 TRP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15150 Z= 0.384 Angle : 0.621 8.871 20654 Z= 0.300 Chirality : 0.043 0.194 2250 Planarity : 0.004 0.038 2648 Dihedral : 7.783 86.214 2088 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.00 % Allowed : 10.21 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1830 helix: 1.85 (0.21), residues: 682 sheet: 0.72 (0.28), residues: 344 loop : -1.27 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 135 HIS 0.009 0.001 HIS D 206 PHE 0.017 0.002 PHE A 510 TYR 0.014 0.002 TYR C 286 ARG 0.009 0.001 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 76 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8791 (mtpt) REVERT: A 414 GLN cc_start: 0.8249 (mt0) cc_final: 0.7450 (mm-40) REVERT: B 380 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8771 (mtpt) REVERT: B 414 GLN cc_start: 0.8276 (mt0) cc_final: 0.7476 (mm-40) REVERT: C 90 ASP cc_start: 0.8261 (m-30) cc_final: 0.8014 (m-30) REVERT: C 162 LYS cc_start: 0.8721 (pttt) cc_final: 0.8243 (tppt) REVERT: C 242 ASP cc_start: 0.8525 (m-30) cc_final: 0.7757 (t0) REVERT: C 245 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8709 (tptp) REVERT: D 90 ASP cc_start: 0.8263 (m-30) cc_final: 0.7851 (m-30) REVERT: D 162 LYS cc_start: 0.8695 (pttt) cc_final: 0.8251 (tppt) REVERT: D 242 ASP cc_start: 0.8524 (m-30) cc_final: 0.7748 (t0) REVERT: D 267 MET cc_start: 0.8206 (mmm) cc_final: 0.7806 (tpp) outliers start: 31 outliers final: 15 residues processed: 103 average time/residue: 1.4203 time to fit residues: 160.5283 Evaluate side-chains 92 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain D residue 24 TRP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 194 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 128 optimal weight: 0.0370 chunk 99 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15150 Z= 0.154 Angle : 0.522 7.140 20654 Z= 0.247 Chirality : 0.038 0.166 2250 Planarity : 0.004 0.035 2648 Dihedral : 7.337 75.085 2088 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.23 % Allowed : 11.43 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1830 helix: 2.12 (0.21), residues: 674 sheet: 0.93 (0.28), residues: 344 loop : -1.15 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 PHE 0.012 0.001 PHE A 510 TYR 0.008 0.001 TYR D 250 ARG 0.008 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7444 (m-40) REVERT: A 414 GLN cc_start: 0.8208 (mt0) cc_final: 0.7440 (mm-40) REVERT: B 215 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7433 (m-40) REVERT: B 414 GLN cc_start: 0.8217 (mt0) cc_final: 0.7457 (mm-40) REVERT: C 90 ASP cc_start: 0.8190 (m-30) cc_final: 0.7908 (m-30) REVERT: C 162 LYS cc_start: 0.8682 (pttt) cc_final: 0.8216 (tppt) REVERT: C 242 ASP cc_start: 0.8483 (m-30) cc_final: 0.7774 (t0) REVERT: C 245 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8671 (tptp) REVERT: C 305 MET cc_start: 0.8637 (mpp) cc_final: 0.8291 (mpt) REVERT: D 90 ASP cc_start: 0.8262 (m-30) cc_final: 0.7891 (m-30) REVERT: D 162 LYS cc_start: 0.8650 (pttt) cc_final: 0.8213 (tppt) REVERT: D 242 ASP cc_start: 0.8481 (m-30) cc_final: 0.7773 (t0) REVERT: D 305 MET cc_start: 0.8616 (mpp) cc_final: 0.8257 (mpt) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 1.4010 time to fit residues: 146.4804 Evaluate side-chains 83 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain D residue 24 TRP Chi-restraints excluded: chain D residue 91 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15150 Z= 0.288 Angle : 0.571 7.816 20654 Z= 0.272 Chirality : 0.041 0.169 2250 Planarity : 0.004 0.035 2648 Dihedral : 7.418 79.607 2088 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.16 % Allowed : 11.76 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1830 helix: 2.00 (0.21), residues: 672 sheet: 0.83 (0.28), residues: 344 loop : -1.15 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 24 HIS 0.008 0.001 HIS C 206 PHE 0.016 0.002 PHE A 510 TYR 0.012 0.001 TYR D 250 ARG 0.008 0.001 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8253 (mt0) cc_final: 0.7463 (mm-40) REVERT: B 414 GLN cc_start: 0.8263 (mt0) cc_final: 0.7479 (mm-40) REVERT: C 90 ASP cc_start: 0.8236 (m-30) cc_final: 0.7945 (m-30) REVERT: C 162 LYS cc_start: 0.8692 (pttt) cc_final: 0.8202 (tppt) REVERT: C 242 ASP cc_start: 0.8506 (m-30) cc_final: 0.7764 (t0) REVERT: C 245 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8723 (tptp) REVERT: C 305 MET cc_start: 0.8594 (mpp) cc_final: 0.8220 (mpt) REVERT: D 90 ASP cc_start: 0.8277 (m-30) cc_final: 0.7909 (m-30) REVERT: D 139 GLN cc_start: 0.8818 (tt0) cc_final: 0.8571 (mp10) REVERT: D 162 LYS cc_start: 0.8644 (pttt) cc_final: 0.8214 (tppt) REVERT: D 242 ASP cc_start: 0.8492 (m-30) cc_final: 0.7750 (t0) REVERT: D 305 MET cc_start: 0.8580 (mpp) cc_final: 0.8195 (mpt) outliers start: 18 outliers final: 15 residues processed: 89 average time/residue: 1.3810 time to fit residues: 135.6683 Evaluate side-chains 87 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain D residue 24 TRP Chi-restraints excluded: chain D residue 91 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 163 optimal weight: 0.0000 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 147 optimal weight: 0.0770 chunk 154 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15150 Z= 0.133 Angle : 0.504 6.283 20654 Z= 0.237 Chirality : 0.038 0.165 2250 Planarity : 0.004 0.033 2648 Dihedral : 7.106 70.890 2088 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.23 % Allowed : 11.89 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1830 helix: 2.19 (0.21), residues: 676 sheet: 0.93 (0.28), residues: 340 loop : -1.07 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 24 HIS 0.005 0.000 HIS D 206 PHE 0.012 0.001 PHE A 510 TYR 0.007 0.001 TYR D 317 ARG 0.009 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7503 (m-40) REVERT: A 414 GLN cc_start: 0.8213 (mt0) cc_final: 0.7477 (mm-40) REVERT: B 215 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7505 (m-40) REVERT: B 414 GLN cc_start: 0.8210 (mt0) cc_final: 0.7477 (mm-40) REVERT: C 90 ASP cc_start: 0.8189 (m-30) cc_final: 0.7927 (m-30) REVERT: C 139 GLN cc_start: 0.8825 (tt0) cc_final: 0.8547 (mp10) REVERT: C 162 LYS cc_start: 0.8636 (pttt) cc_final: 0.8168 (tppt) REVERT: C 242 ASP cc_start: 0.8478 (m-30) cc_final: 0.7785 (t0) REVERT: C 245 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8692 (tptp) REVERT: C 305 MET cc_start: 0.8568 (mpp) cc_final: 0.8183 (mpt) REVERT: D 90 ASP cc_start: 0.8214 (m-30) cc_final: 0.7858 (m-30) REVERT: D 139 GLN cc_start: 0.8819 (tt0) cc_final: 0.8536 (mp10) REVERT: D 162 LYS cc_start: 0.8622 (pttt) cc_final: 0.8168 (tppt) REVERT: D 242 ASP cc_start: 0.8456 (m-30) cc_final: 0.7766 (t0) REVERT: D 305 MET cc_start: 0.8553 (mpp) cc_final: 0.8204 (mpt) outliers start: 19 outliers final: 11 residues processed: 100 average time/residue: 1.3564 time to fit residues: 149.8912 Evaluate side-chains 88 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 24 TRP Chi-restraints excluded: chain D residue 91 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 82 optimal weight: 0.0030 chunk 120 optimal weight: 0.9990 chunk 181 optimal weight: 0.3980 chunk 166 optimal weight: 0.0470 chunk 144 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.4690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN D 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15150 Z= 0.149 Angle : 0.527 7.304 20654 Z= 0.250 Chirality : 0.038 0.164 2250 Planarity : 0.004 0.034 2648 Dihedral : 7.013 72.120 2088 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.78 % Allowed : 12.66 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1830 helix: 2.16 (0.21), residues: 674 sheet: 0.97 (0.28), residues: 340 loop : -1.01 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 24 HIS 0.004 0.000 HIS C 206 PHE 0.013 0.001 PHE A 510 TYR 0.007 0.001 TYR D 250 ARG 0.009 0.000 ARG D 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8207 (mt0) cc_final: 0.7469 (mm-40) REVERT: B 414 GLN cc_start: 0.8217 (mt0) cc_final: 0.7475 (mm-40) REVERT: C 90 ASP cc_start: 0.8203 (m-30) cc_final: 0.7941 (m-30) REVERT: C 162 LYS cc_start: 0.8638 (pttt) cc_final: 0.8163 (tppt) REVERT: C 242 ASP cc_start: 0.8464 (m-30) cc_final: 0.7792 (t0) REVERT: C 245 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8680 (tptp) REVERT: C 305 MET cc_start: 0.8567 (mpp) cc_final: 0.8209 (mpt) REVERT: D 90 ASP cc_start: 0.8208 (m-30) cc_final: 0.7848 (m-30) REVERT: D 162 LYS cc_start: 0.8638 (pttt) cc_final: 0.8182 (tppt) REVERT: D 242 ASP cc_start: 0.8453 (m-30) cc_final: 0.7761 (t0) REVERT: D 305 MET cc_start: 0.8564 (mpp) cc_final: 0.8218 (mpt) outliers start: 12 outliers final: 13 residues processed: 87 average time/residue: 1.4467 time to fit residues: 138.2075 Evaluate side-chains 87 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 24 TRP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 0.0670 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 144 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.092032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065266 restraints weight = 29955.023| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.06 r_work: 0.2891 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15150 Z= 0.176 Angle : 0.542 9.169 20654 Z= 0.256 Chirality : 0.039 0.165 2250 Planarity : 0.004 0.056 2648 Dihedral : 7.020 71.222 2088 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.90 % Allowed : 12.73 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1830 helix: 2.12 (0.21), residues: 674 sheet: 0.96 (0.28), residues: 340 loop : -1.00 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 24 HIS 0.005 0.001 HIS C 206 PHE 0.013 0.001 PHE A 510 TYR 0.009 0.001 TYR D 250 ARG 0.014 0.000 ARG C 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4511.89 seconds wall clock time: 80 minutes 54.30 seconds (4854.30 seconds total)