Starting phenix.real_space_refine on Thu Jun 27 14:54:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/06_2024/8ut7_42532_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/06_2024/8ut7_42532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/06_2024/8ut7_42532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/06_2024/8ut7_42532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/06_2024/8ut7_42532_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut7_42532/06_2024/8ut7_42532_updated.pdb" } resolution = 2.7 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= 0.027 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8094 2.51 5 N 2314 2.21 5 O 2584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "E GLU 344": "OE1" <-> "OE2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "E GLU 449": "OE1" <-> "OE2" Residue "E GLU 457": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 13046 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "H" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "E" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3843 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 8.86, per 1000 atoms: 0.68 Number of scatterers: 13046 At special positions: 0 Unit cell: (116, 91.35, 140.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2584 8.00 N 2314 7.00 C 8094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.02 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=1.17 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E 466 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.04 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 477 " distance=2.89 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=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 38 " " NAG A 602 " - " ASN A 63 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 246 " " NAG A 605 " - " ASN A 285 " " NAG A 606 " - " ASN A 483 " " NAG B 1 " - " ASN A 165 " " NAG C 601 " - " ASN C 38 " " NAG C 602 " - " ASN C 63 " " NAG C 603 " - " ASN C 133 " " NAG C 604 " - " ASN C 246 " " NAG C 605 " - " ASN C 285 " " NAG C 606 " - " ASN C 483 " " NAG D 1 " - " ASN C 165 " " NAG E 601 " - " ASN E 38 " " NAG E 602 " - " ASN E 63 " " NAG E 603 " - " ASN E 133 " " NAG E 604 " - " ASN E 246 " " NAG E 605 " - " ASN E 285 " " NAG E 606 " - " ASN E 483 " " NAG F 1 " - " ASN E 165 " Time building additional restraints: 4.99 Conformation dependent library (CDL) restraints added in 2.0 seconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 35 sheets defined 25.2% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 109 through 112 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 74 through 79 removed outlier: 4.831A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 405 through 455 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.847A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLY C 78 " --> pdb=" O GLN C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'C' and resid 367 through 384 Processing helix chain 'C' and resid 405 through 455 Processing helix chain 'C' and resid 475 through 482 Processing helix chain 'C' and resid 492 through 499 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 74 through 79 removed outlier: 3.737A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLY E 78 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 115 Processing helix chain 'E' and resid 188 through 195 Processing helix chain 'E' and resid 367 through 384 Processing helix chain 'E' and resid 405 through 458 removed outlier: 6.722A pdb=" N GLU E 457 " --> pdb=" O LYS E 453 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN E 458 " --> pdb=" O GLN E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 482 Processing helix chain 'E' and resid 492 through 499 Processing sheet with id= A, first strand: chain 'G' and resid 3 through 6 Processing sheet with id= B, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.187A pdb=" N UNK G 38 " --> pdb=" O UNK G 47 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N UNK G 47 " --> pdb=" O UNK G 38 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N UNK G 40 " --> pdb=" O UNK G 45 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N UNK G 45 " --> pdb=" O UNK G 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 4 through 6 Processing sheet with id= D, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.575A pdb=" N UNK H 105 " --> pdb=" O UNK H 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'H' and resid 98 through 100 removed outlier: 5.951A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 361 through 366 removed outlier: 4.456A pdb=" N TYR A 351 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 24 through 26 Processing sheet with id= H, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= I, first strand: chain 'A' and resid 50 through 52 No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.782A pdb=" N LEU A 86 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SER A 266 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLU A 89 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET A 268 " --> pdb=" O GLU A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 120 through 122 Processing sheet with id= L, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= M, first strand: chain 'A' and resid 164 through 169 Processing sheet with id= N, first strand: chain 'A' and resid 176 through 184 Processing sheet with id= O, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.278A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 136 through 141 removed outlier: 3.696A pdb=" N SER A 146 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 9.828A pdb=" N LYS A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 361 through 366 removed outlier: 4.469A pdb=" N TYR C 351 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 24 through 26 Processing sheet with id= S, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= T, first strand: chain 'C' and resid 50 through 52 No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.779A pdb=" N LEU C 86 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER C 266 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLU C 89 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N MET C 268 " --> pdb=" O GLU C 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'C' and resid 120 through 122 Processing sheet with id= W, first strand: chain 'C' and resid 151 through 153 Processing sheet with id= X, first strand: chain 'C' and resid 164 through 169 Processing sheet with id= Y, first strand: chain 'C' and resid 176 through 184 Processing sheet with id= Z, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.309A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 305 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 361 through 365 Processing sheet with id= AB, first strand: chain 'E' and resid 24 through 26 Processing sheet with id= AC, first strand: chain 'E' and resid 39 through 41 Processing sheet with id= AD, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.617A pdb=" N LEU E 86 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER E 266 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLU E 89 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N MET E 268 " --> pdb=" O GLU E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.246A pdb=" N ILE E 230 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 120 through 122 Processing sheet with id= AG, first strand: chain 'E' and resid 151 through 153 Processing sheet with id= AH, first strand: chain 'E' and resid 164 through 169 Processing sheet with id= AI, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.344A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1323 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: 4.02 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 4497 1.37 - 1.51: 3755 1.51 - 1.66: 4957 1.66 - 1.80: 43 1.80 - 1.95: 29 Bond restraints: 13281 Sorted by residual: bond pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " ideal model delta sigma weight residual 1.808 1.946 -0.138 3.30e-02 9.18e+02 1.76e+01 bond pdb=" N CYS E 477 " pdb=" CA CYS E 477 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.77e+00 bond pdb=" N ASP E 474 " pdb=" CA ASP E 474 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.27e-02 6.20e+03 7.39e+00 bond pdb=" N CYS C 277 " pdb=" CA CYS C 277 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.29e-02 6.01e+03 7.00e+00 bond pdb=" N ASN C 278 " pdb=" CA ASN C 278 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.23e-02 6.61e+03 6.88e+00 ... (remaining 13276 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.22: 528 107.22 - 113.92: 7229 113.92 - 120.62: 5244 120.62 - 127.32: 4874 127.32 - 134.02: 152 Bond angle restraints: 18027 Sorted by residual: angle pdb=" C PRO C 324 " pdb=" N GLU C 325 " pdb=" CA GLU C 325 " ideal model delta sigma weight residual 121.70 129.64 -7.94 1.80e+00 3.09e-01 1.94e+01 angle pdb=" CA ALA E 476 " pdb=" C ALA E 476 " pdb=" O ALA E 476 " ideal model delta sigma weight residual 120.55 116.05 4.50 1.06e+00 8.90e-01 1.80e+01 angle pdb=" CG ARG C 321 " pdb=" CD ARG C 321 " pdb=" NE ARG C 321 " ideal model delta sigma weight residual 112.00 120.90 -8.90 2.20e+00 2.07e-01 1.64e+01 angle pdb=" C ARG A 456 " pdb=" CA ARG A 456 " pdb=" CB ARG A 456 " ideal model delta sigma weight residual 117.23 111.73 5.50 1.36e+00 5.41e-01 1.64e+01 angle pdb=" C CYS C 52 " pdb=" CA CYS C 52 " pdb=" CB CYS C 52 " ideal model delta sigma weight residual 109.53 116.11 -6.58 1.65e+00 3.67e-01 1.59e+01 ... (remaining 18022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 7808 16.99 - 33.99: 326 33.99 - 50.98: 131 50.98 - 67.98: 51 67.98 - 84.97: 14 Dihedral angle restraints: 8330 sinusoidal: 3421 harmonic: 4909 Sorted by residual: dihedral pdb=" CB CYS E 64 " pdb=" SG CYS E 64 " pdb=" SG CYS E 76 " pdb=" CB CYS E 76 " ideal model delta sinusoidal sigma weight residual -86.00 -125.47 39.47 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" CA CYS A 97 " pdb=" CB CYS A 97 " pdb=" SG CYS A 97 " pdb=" SG CYS A 139 " ideal model delta sinusoidal sigma weight residual 79.00 3.13 75.87 1 2.00e+01 2.50e-03 1.81e+01 dihedral pdb=" CA CYS C 97 " pdb=" CB CYS C 97 " pdb=" SG CYS C 97 " pdb=" SG CYS C 139 " ideal model delta sinusoidal sigma weight residual -73.00 -1.24 -71.76 1 2.00e+01 2.50e-03 1.65e+01 ... (remaining 8327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1280 0.044 - 0.088: 523 0.088 - 0.132: 206 0.132 - 0.176: 63 0.176 - 0.220: 10 Chirality restraints: 2082 Sorted by residual: chirality pdb=" C1 NAG E 604 " pdb=" ND2 ASN E 246 " pdb=" C2 NAG E 604 " pdb=" O5 NAG E 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA UNK G 99 " pdb=" N UNK G 99 " pdb=" C UNK G 99 " pdb=" CB UNK G 99 " both_signs ideal model delta sigma weight residual False 2.52 2.32 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2079 not shown) Planarity restraints: 2378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 477 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C CYS E 477 " 0.059 2.00e-02 2.50e+03 pdb=" O CYS E 477 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE E 478 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 74 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C PRO A 74 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO A 74 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 75 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK H 69 " -0.014 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C UNK H 69 " 0.052 2.00e-02 2.50e+03 pdb=" O UNK H 69 " -0.020 2.00e-02 2.50e+03 pdb=" N UNK H 70 " -0.018 2.00e-02 2.50e+03 ... (remaining 2375 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 787 2.72 - 3.26: 12293 3.26 - 3.81: 21903 3.81 - 4.35: 28122 4.35 - 4.90: 46504 Nonbonded interactions: 109609 Sorted by model distance: nonbonded pdb=" O GLY E 218 " pdb=" NH1 ARG E 220 " model vdw 2.173 2.520 nonbonded pdb=" OE2 GLU A 401 " pdb=" CD ARG E 208 " model vdw 2.181 3.440 nonbonded pdb=" OD2 ASP A 408 " pdb=" OG SER E 110 " model vdw 2.266 2.440 nonbonded pdb=" OE1 GLU A 457 " pdb=" NH2 ARG A 499 " model vdw 2.297 2.520 nonbonded pdb=" OG SER A 110 " pdb=" OD2 ASP C 408 " model vdw 2.306 2.440 ... (remaining 109604 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' and (resid 8 through 501 or resid 601 through 606)) selection = (chain 'C' and (resid 8 through 501 or resid 601 through 606)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 5.230 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: 17.600 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 38.300 Find NCS groups from input model: 0.810 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: 0.010 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.006 0.138 13281 Z= 0.401 Angle : 1.096 12.682 18027 Z= 0.609 Chirality : 0.057 0.220 2082 Planarity : 0.006 0.046 2357 Dihedral : 12.342 84.973 5106 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.80 (0.19), residues: 1448 helix: 1.57 (0.23), residues: 354 sheet: 0.56 (0.27), residues: 302 loop : 0.13 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP E 127 HIS 0.010 0.002 HIS A 156 PHE 0.019 0.003 PHE A 353 TYR 0.021 0.004 TYR C 195 ARG 0.019 0.002 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8410 (p) cc_final: 0.8035 (m) REVERT: A 380 LYS cc_start: 0.7506 (mtmm) cc_final: 0.6866 (mtmm) REVERT: A 401 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6714 (mm-30) REVERT: A 432 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8134 (mm-30) REVERT: C 104 ASP cc_start: 0.8019 (t0) cc_final: 0.7731 (t0) REVERT: C 356 GLN cc_start: 0.7594 (tp-100) cc_final: 0.7296 (tp40) REVERT: C 367 LEU cc_start: 0.8686 (mt) cc_final: 0.8193 (mt) REVERT: C 383 ARG cc_start: 0.7552 (ptm-80) cc_final: 0.6644 (ptt90) REVERT: C 498 ASN cc_start: 0.8090 (m-40) cc_final: 0.7887 (m110) REVERT: E 75 GLN cc_start: 0.7712 (mt0) cc_final: 0.7484 (mt0) REVERT: E 344 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7385 (mp0) REVERT: E 359 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6971 (mt-10) REVERT: E 475 ASN cc_start: 0.7367 (m-40) cc_final: 0.6820 (m110) outliers start: 0 outliers final: 1 residues processed: 163 average time/residue: 1.3586 time to fit residues: 240.0831 Evaluate side-chains 136 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.0670 chunk 42 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 197 GLN A 355 HIS A 454 GLN C 158 ASN C 407 GLN C 435 HIS C 454 GLN E 435 HIS E 488 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13281 Z= 0.179 Angle : 0.547 7.818 18027 Z= 0.289 Chirality : 0.042 0.225 2082 Planarity : 0.004 0.036 2357 Dihedral : 4.790 36.997 2314 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.64 % Allowed : 7.52 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.01 (0.20), residues: 1448 helix: 2.48 (0.24), residues: 354 sheet: 0.24 (0.27), residues: 304 loop : 0.08 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.003 0.001 HIS C 184 PHE 0.012 0.002 PHE A 353 TYR 0.013 0.001 TYR A 195 ARG 0.006 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8198 (m-30) cc_final: 0.7818 (m-30) REVERT: A 142 ARG cc_start: 0.7910 (mtt-85) cc_final: 0.7662 (mtt90) REVERT: A 144 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.6998 (ptmt) REVERT: A 310 LYS cc_start: 0.8709 (mttt) cc_final: 0.8365 (mtmt) REVERT: A 346 MET cc_start: 0.7572 (ttp) cc_final: 0.7251 (ttp) REVERT: A 401 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6813 (mm-30) REVERT: A 460 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: C 104 ASP cc_start: 0.8134 (t0) cc_final: 0.7774 (t0) REVERT: C 119 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8155 (mt-10) REVERT: C 201 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7767 (ptt90) REVERT: C 383 ARG cc_start: 0.7677 (ptm-80) cc_final: 0.6848 (ptt90) REVERT: E 315 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8166 (mmtt) outliers start: 21 outliers final: 5 residues processed: 161 average time/residue: 1.4147 time to fit residues: 246.0730 Evaluate side-chains 140 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 339 ILE Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 31 ASN A 296 ASN A 312 ASN C 122 ASN C 158 ASN C 407 GLN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13281 Z= 0.385 Angle : 0.630 11.495 18027 Z= 0.325 Chirality : 0.046 0.252 2082 Planarity : 0.005 0.042 2357 Dihedral : 5.226 30.406 2312 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.35 % Allowed : 8.61 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.30 (0.20), residues: 1448 helix: 2.19 (0.25), residues: 345 sheet: -0.26 (0.27), residues: 304 loop : -0.48 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 421 HIS 0.007 0.002 HIS E 18 PHE 0.017 0.002 PHE A 353 TYR 0.015 0.002 TYR C 195 ARG 0.011 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8392 (m-30) cc_final: 0.7964 (m-30) REVERT: A 142 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7661 (mtt90) REVERT: A 144 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7086 (ptmt) REVERT: A 310 LYS cc_start: 0.8731 (mttt) cc_final: 0.8333 (mtmt) REVERT: A 346 MET cc_start: 0.7845 (ttp) cc_final: 0.7334 (ttp) REVERT: A 401 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6844 (mm-30) REVERT: A 460 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: C 104 ASP cc_start: 0.8331 (t0) cc_final: 0.8049 (t0) REVERT: C 111 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7522 (tp) REVERT: C 344 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6696 (mp0) REVERT: E 201 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7904 (ttp-170) REVERT: E 415 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7654 (m-30) outliers start: 30 outliers final: 12 residues processed: 165 average time/residue: 1.4841 time to fit residues: 264.5339 Evaluate side-chains 149 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 143 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 376 GLN A 389 ASN C 33 GLN C 158 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13281 Z= 0.182 Angle : 0.495 9.149 18027 Z= 0.257 Chirality : 0.041 0.222 2082 Planarity : 0.004 0.038 2357 Dihedral : 4.727 24.978 2312 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.64 % Allowed : 10.10 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1448 helix: 2.34 (0.26), residues: 347 sheet: -0.30 (0.27), residues: 291 loop : -0.50 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 421 HIS 0.002 0.001 HIS C 184 PHE 0.017 0.001 PHE C 338 TYR 0.010 0.001 TYR A 195 ARG 0.005 0.000 ARG C 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6612 (t0) cc_final: 0.5969 (m-40) REVERT: A 104 ASP cc_start: 0.8323 (m-30) cc_final: 0.7917 (m-30) REVERT: A 142 ARG cc_start: 0.7887 (mtt-85) cc_final: 0.7645 (mtt90) REVERT: A 310 LYS cc_start: 0.8700 (mttt) cc_final: 0.8348 (mtmt) REVERT: A 346 MET cc_start: 0.7818 (ttp) cc_final: 0.7394 (ttp) REVERT: A 401 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6786 (tm-30) REVERT: A 460 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: C 104 ASP cc_start: 0.8303 (t0) cc_final: 0.8007 (t0) REVERT: C 111 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7356 (tp) REVERT: C 344 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6701 (mp0) REVERT: C 453 LYS cc_start: 0.7987 (mttm) cc_final: 0.7761 (mttm) REVERT: E 92 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8061 (pttm) REVERT: E 208 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7592 (ttp-170) REVERT: E 315 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8278 (mmtt) REVERT: E 415 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7575 (t70) outliers start: 21 outliers final: 8 residues processed: 150 average time/residue: 1.4655 time to fit residues: 236.9202 Evaluate side-chains 142 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN C 407 GLN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13281 Z= 0.238 Angle : 0.515 9.671 18027 Z= 0.265 Chirality : 0.042 0.230 2082 Planarity : 0.004 0.038 2357 Dihedral : 4.711 24.825 2312 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.57 % Allowed : 10.49 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.28 (0.20), residues: 1448 helix: 2.37 (0.26), residues: 348 sheet: -0.54 (0.28), residues: 269 loop : -0.50 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 421 HIS 0.005 0.001 HIS E 18 PHE 0.016 0.001 PHE C 338 TYR 0.012 0.002 TYR C 105 ARG 0.007 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6615 (t0) cc_final: 0.5950 (m-40) REVERT: A 104 ASP cc_start: 0.8342 (m-30) cc_final: 0.7905 (m-30) REVERT: A 142 ARG cc_start: 0.7878 (mtt-85) cc_final: 0.7632 (mtt90) REVERT: A 276 LYS cc_start: 0.8079 (mptt) cc_final: 0.7469 (ttpt) REVERT: A 310 LYS cc_start: 0.8693 (mttt) cc_final: 0.8319 (mtmt) REVERT: A 346 MET cc_start: 0.7853 (ttp) cc_final: 0.7487 (ttp) REVERT: A 401 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6797 (tm-30) REVERT: A 460 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: C 111 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7349 (tp) REVERT: C 344 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6659 (mp0) REVERT: C 401 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: C 453 LYS cc_start: 0.8062 (mttm) cc_final: 0.7825 (mttm) REVERT: E 32 ASP cc_start: 0.6833 (t0) cc_final: 0.6516 (t70) REVERT: E 208 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7660 (ttp-170) REVERT: E 415 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7647 (m-30) outliers start: 20 outliers final: 10 residues processed: 142 average time/residue: 1.5068 time to fit residues: 230.3778 Evaluate side-chains 144 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 84 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13281 Z= 0.255 Angle : 0.516 10.142 18027 Z= 0.265 Chirality : 0.042 0.232 2082 Planarity : 0.004 0.038 2357 Dihedral : 4.805 25.253 2312 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.57 % Allowed : 11.28 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.20 (0.20), residues: 1448 helix: 2.30 (0.26), residues: 348 sheet: -0.61 (0.28), residues: 269 loop : -0.54 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.004 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.013 0.002 TYR C 105 ARG 0.008 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6641 (t0) cc_final: 0.5972 (m-40) REVERT: A 50 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7167 (pt0) REVERT: A 92 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7556 (mtpp) REVERT: A 104 ASP cc_start: 0.8363 (m-30) cc_final: 0.7918 (m-30) REVERT: A 276 LYS cc_start: 0.8106 (mptt) cc_final: 0.7506 (ttpt) REVERT: A 310 LYS cc_start: 0.8699 (mttt) cc_final: 0.8319 (mtmt) REVERT: A 346 MET cc_start: 0.7825 (ttp) cc_final: 0.7479 (ttp) REVERT: A 389 ASN cc_start: 0.7481 (m-40) cc_final: 0.6123 (p0) REVERT: A 401 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6831 (tm-30) REVERT: A 460 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: C 111 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7379 (tp) REVERT: C 201 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7831 (ptt90) REVERT: C 344 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6647 (mp0) REVERT: E 32 ASP cc_start: 0.6888 (t0) cc_final: 0.6610 (t70) REVERT: E 208 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7806 (ttp-170) REVERT: E 315 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8300 (mmtt) REVERT: E 415 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7571 (t70) outliers start: 20 outliers final: 9 residues processed: 141 average time/residue: 1.4917 time to fit residues: 226.5046 Evaluate side-chains 143 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN C 407 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13281 Z= 0.335 Angle : 0.563 10.925 18027 Z= 0.286 Chirality : 0.044 0.238 2082 Planarity : 0.004 0.041 2357 Dihedral : 5.096 30.306 2312 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.04 % Allowed : 11.20 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.07 (0.20), residues: 1448 helix: 2.17 (0.26), residues: 348 sheet: -0.67 (0.28), residues: 269 loop : -0.61 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 234 HIS 0.005 0.001 HIS E 18 PHE 0.016 0.002 PHE C 338 TYR 0.014 0.002 TYR C 105 ARG 0.007 0.001 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6694 (t0) cc_final: 0.5991 (m-40) REVERT: A 50 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7204 (pt0) REVERT: A 92 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7478 (mtpp) REVERT: A 104 ASP cc_start: 0.8400 (m-30) cc_final: 0.7928 (m-30) REVERT: A 276 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7567 (ttpt) REVERT: A 310 LYS cc_start: 0.8710 (mttt) cc_final: 0.8330 (mtmt) REVERT: A 346 MET cc_start: 0.7819 (ttp) cc_final: 0.7567 (ttp) REVERT: A 389 ASN cc_start: 0.7531 (m-40) cc_final: 0.6149 (p0) REVERT: A 401 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6795 (tm-30) REVERT: A 460 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: C 201 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7809 (ptt90) REVERT: C 344 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6648 (mp0) REVERT: C 401 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: E 32 ASP cc_start: 0.6911 (t0) cc_final: 0.6705 (t70) REVERT: E 208 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7825 (ttp-170) REVERT: E 315 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8290 (mmtt) REVERT: E 415 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7629 (m-30) outliers start: 26 outliers final: 15 residues processed: 144 average time/residue: 1.4743 time to fit residues: 228.7950 Evaluate side-chains 146 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13281 Z= 0.327 Angle : 0.559 11.172 18027 Z= 0.285 Chirality : 0.043 0.236 2082 Planarity : 0.004 0.040 2357 Dihedral : 5.234 34.348 2312 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.19 % Allowed : 11.51 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.01 (0.20), residues: 1448 helix: 2.06 (0.26), residues: 348 sheet: -0.55 (0.28), residues: 289 loop : -0.68 (0.19), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 421 HIS 0.005 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.014 0.002 TYR C 105 ARG 0.008 0.001 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6667 (t0) cc_final: 0.5992 (m-40) REVERT: A 50 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7264 (pt0) REVERT: A 92 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7457 (mtpp) REVERT: A 104 ASP cc_start: 0.8377 (m-30) cc_final: 0.7899 (m-30) REVERT: A 276 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7620 (ttpt) REVERT: A 310 LYS cc_start: 0.8710 (mttt) cc_final: 0.8332 (mtmt) REVERT: A 389 ASN cc_start: 0.7561 (m-40) cc_final: 0.6128 (p0) REVERT: A 401 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6878 (tm-30) REVERT: C 201 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7831 (ptt90) REVERT: C 344 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6678 (mp0) REVERT: E 208 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7851 (ttp-170) REVERT: E 315 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8289 (mmtt) REVERT: E 356 GLN cc_start: 0.7640 (tt0) cc_final: 0.7397 (tt0) REVERT: E 415 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7627 (m-30) outliers start: 28 outliers final: 18 residues processed: 143 average time/residue: 1.4862 time to fit residues: 228.8090 Evaluate side-chains 150 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 6.9990 chunk 139 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN C 407 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13281 Z= 0.204 Angle : 0.493 9.471 18027 Z= 0.254 Chirality : 0.042 0.225 2082 Planarity : 0.004 0.038 2357 Dihedral : 4.867 29.963 2312 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.72 % Allowed : 11.82 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.11 (0.20), residues: 1448 helix: 2.24 (0.26), residues: 348 sheet: -0.78 (0.28), residues: 275 loop : -0.55 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS E 18 PHE 0.016 0.001 PHE C 338 TYR 0.012 0.001 TYR C 105 ARG 0.008 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6635 (t0) cc_final: 0.6025 (m-40) REVERT: A 50 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7266 (pt0) REVERT: A 92 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7452 (mtpp) REVERT: A 104 ASP cc_start: 0.8362 (m-30) cc_final: 0.7890 (m-30) REVERT: A 276 LYS cc_start: 0.8190 (mptt) cc_final: 0.7605 (ttpt) REVERT: A 310 LYS cc_start: 0.8701 (mttt) cc_final: 0.8327 (mtmt) REVERT: A 389 ASN cc_start: 0.7506 (m-40) cc_final: 0.6120 (p0) REVERT: A 401 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6879 (tm-30) REVERT: C 201 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7702 (ptt90) REVERT: C 280 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: E 208 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7821 (ttp-170) REVERT: E 315 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8278 (mmtt) REVERT: E 356 GLN cc_start: 0.7624 (tt0) cc_final: 0.7387 (tt0) REVERT: E 415 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7525 (t70) outliers start: 22 outliers final: 13 residues processed: 140 average time/residue: 1.5140 time to fit residues: 227.9625 Evaluate side-chains 141 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 152 optimal weight: 0.0570 chunk 131 optimal weight: 0.0770 chunk 13 optimal weight: 30.0000 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13281 Z= 0.145 Angle : 0.454 7.612 18027 Z= 0.236 Chirality : 0.041 0.216 2082 Planarity : 0.004 0.037 2357 Dihedral : 4.436 22.259 2312 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.49 % Allowed : 12.06 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.26 (0.21), residues: 1448 helix: 2.40 (0.26), residues: 349 sheet: -0.68 (0.28), residues: 275 loop : -0.49 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 421 HIS 0.002 0.001 HIS A 156 PHE 0.016 0.001 PHE C 338 TYR 0.010 0.001 TYR C 105 ARG 0.008 0.000 ARG C 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6624 (t0) cc_final: 0.6054 (m-40) REVERT: A 50 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7208 (pt0) REVERT: A 92 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7439 (mtpp) REVERT: A 104 ASP cc_start: 0.8290 (m-30) cc_final: 0.7835 (m-30) REVERT: A 276 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7590 (ttpt) REVERT: A 310 LYS cc_start: 0.8705 (mttt) cc_final: 0.8345 (mtmt) REVERT: A 389 ASN cc_start: 0.7424 (m-40) cc_final: 0.6104 (p0) REVERT: A 401 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6878 (tm-30) REVERT: C 104 ASP cc_start: 0.8204 (t0) cc_final: 0.7937 (t0) REVERT: C 280 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: E 32 ASP cc_start: 0.6987 (t70) cc_final: 0.6250 (p0) REVERT: E 208 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7780 (ttp-170) REVERT: E 315 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8288 (mmtt) REVERT: E 415 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7515 (t70) outliers start: 19 outliers final: 10 residues processed: 151 average time/residue: 1.4519 time to fit residues: 236.5448 Evaluate side-chains 146 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN C 407 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120406 restraints weight = 13623.597| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.55 r_work: 0.3207 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13281 Z= 0.402 Angle : 0.594 11.583 18027 Z= 0.303 Chirality : 0.045 0.234 2082 Planarity : 0.004 0.040 2357 Dihedral : 5.214 33.514 2312 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.41 % Allowed : 12.45 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.02 (0.20), residues: 1448 helix: 2.04 (0.26), residues: 349 sheet: -0.59 (0.28), residues: 294 loop : -0.64 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 234 HIS 0.006 0.001 HIS E 18 PHE 0.014 0.002 PHE A 120 TYR 0.014 0.002 TYR C 105 ARG 0.011 0.001 ARG A 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4624.55 seconds wall clock time: 82 minutes 0.86 seconds (4920.86 seconds total)