Starting phenix.real_space_refine on Tue Mar 19 02:56:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/03_2024/8psz_17865_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/03_2024/8psz_17865.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/03_2024/8psz_17865_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/03_2024/8psz_17865_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/03_2024/8psz_17865_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/03_2024/8psz_17865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/03_2024/8psz_17865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/03_2024/8psz_17865_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psz_17865/03_2024/8psz_17865_trim_updated.pdb" } resolution = 2.42 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= 0.002 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: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 56 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 7221 2.51 5 N 2077 2.21 5 O 2481 1.98 5 H 11195 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23098 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6653 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 513, 7925 Classifications: {'peptide': 513} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 513, 7925 Classifications: {'peptide': 513} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 1 bond proxies already assigned to first conformer: 7960 Chain: "C" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 6652 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 22, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 7} Chain: "S" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 422 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 12} Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 411 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "D" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 453 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, 'A0I': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "V" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 46.840 53.436 18.382 1.00 20.80 S ATOM 4474 SG CYS A 282 44.558 52.018 15.484 1.00 21.12 S ATOM 18191 SG CYS C 233 23.667 63.533 108.687 1.00 68.90 S ATOM 18215 SG CYS C 235 23.744 64.404 104.935 1.00 63.55 S ATOM 16857 SG CYS C 146 12.028 72.706 88.850 1.00 71.81 S ATOM 17045 SG CYS C 159 13.000 75.499 90.912 1.00 66.96 S ATOM 17101 SG CYS C 163 15.366 72.687 90.646 1.00 60.91 S ATOM 17111 SG CYS C 164 14.711 75.039 87.428 1.00 64.71 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AASP B 213 " occ=0.50 ... (22 atoms not shown) pdb=" HB3BASP B 213 " occ=0.50 residue: pdb=" N ATYR B 393 " occ=0.60 ... (40 atoms not shown) pdb=" HH BTYR B 393 " occ=0.40 Time building chain proxies: 11.59, per 1000 atoms: 0.50 Number of scatterers: 23098 At special positions: 0 Unit cell: (92.4, 109.2, 125.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 63 16.00 P 56 15.00 Mg 2 11.99 O 2481 8.00 N 2077 7.00 C 7221 6.00 H 11195 1.00 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=0, symmetry=0 Time building additional restraints: 19.95 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 233 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 235 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " Number of angles added : 9 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 11 sheets defined 35.6% alpha, 10.8% beta 15 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 11.69 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 4.515A pdb=" N GLN A 7 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 175 through 188 Processing helix chain 'A' and resid 224 through 235 removed outlier: 3.596A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 313 through 323 removed outlier: 4.483A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 395 through 414 Processing helix chain 'B' and resid 2 through 4 No H-bonds generated for 'chain 'B' and resid 2 through 4' Processing helix chain 'B' and resid 24 through 38 Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 130 through 136 Processing helix chain 'B' and resid 162 through 182 removed outlier: 3.646A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.728A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 357 through 371 Processing helix chain 'B' and resid 377 through 395 Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 430 through 435 removed outlier: 4.035A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 453 Processing helix chain 'B' and resid 480 through 497 Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 34 through 53 removed outlier: 5.733A pdb=" N SER C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 88 through 96 Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 209 through 218 Processing helix chain 'C' and resid 235 through 240 Processing helix chain 'C' and resid 282 through 288 Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 320 through 333 Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 422 through 425 No H-bonds generated for 'chain 'C' and resid 422 through 425' Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.164A pdb=" N VAL A 69 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU A 56 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N CYS A 71 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.561A pdb=" N ALA A 251 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLN A 200 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N TYR A 202 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET A 255 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 241 through 243 Processing sheet with id= D, first strand: chain 'B' and resid 74 through 79 Processing sheet with id= E, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.472A pdb=" N CYS B 250 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N CYS B 142 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU B 252 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N LEU B 144 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 209 through 211 Processing sheet with id= G, first strand: chain 'B' and resid 326 through 329 Processing sheet with id= H, first strand: chain 'C' and resid 77 through 83 Processing sheet with id= I, first strand: chain 'C' and resid 221 through 224 removed outlier: 3.660A pdb=" N CYS C 259 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL C 264 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 360 through 363 Processing sheet with id= K, first strand: chain 'C' and resid 405 through 409 removed outlier: 3.657A pdb=" N SER C 388 " --> pdb=" O MET C 415 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU C 417 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL C 386 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER C 419 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL C 384 " --> pdb=" O SER C 419 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 8.94 Time building geometry restraints manager: 20.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11163 1.03 - 1.23: 52 1.23 - 1.42: 5191 1.42 - 1.62: 6842 1.62 - 1.81: 89 Bond restraints: 23337 Sorted by residual: bond pdb=" C6 A0I B 601 " pdb=" C7 A0I B 601 " ideal model delta sigma weight residual 1.302 1.531 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C1 A0I B 601 " pdb=" C2 A0I B 601 " ideal model delta sigma weight residual 1.493 1.341 0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C4 A0I B 601 " pdb=" N3 A0I B 601 " ideal model delta sigma weight residual 1.475 1.324 0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C3 A0I B 601 " pdb=" N2 A0I B 601 " ideal model delta sigma weight residual 1.499 1.353 0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" C5 A0I B 601 " pdb=" O2 A0I B 601 " ideal model delta sigma weight residual 1.297 1.411 -0.114 2.00e-02 2.50e+03 3.23e+01 ... (remaining 23332 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 782 107.15 - 113.86: 27437 113.86 - 120.58: 7772 120.58 - 127.29: 5905 127.29 - 134.01: 227 Bond angle restraints: 42123 Sorted by residual: angle pdb=" P1 A0I B 601 " pdb=" N4 A0I B 601 " pdb=" P2 A0I B 601 " ideal model delta sigma weight residual 120.05 131.32 -11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" P2 A0I B 601 " pdb=" O7 A0I B 601 " pdb=" P3 A0I B 601 " ideal model delta sigma weight residual 123.66 133.77 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" O5 A0I B 601 " pdb=" P2 A0I B 601 " pdb=" O6 A0I B 601 " ideal model delta sigma weight residual 109.46 118.73 -9.27 3.00e+00 1.11e-01 9.55e+00 angle pdb=" O11 A0I B 601 " pdb=" P1 A0I B 601 " pdb=" O4 A0I B 601 " ideal model delta sigma weight residual 109.44 118.39 -8.95 3.00e+00 1.11e-01 8.89e+00 angle pdb=" N PRO C 234 " pdb=" CA PRO C 234 " pdb=" CB PRO C 234 " ideal model delta sigma weight residual 103.25 100.43 2.82 1.05e+00 9.07e-01 7.19e+00 ... (remaining 42118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 10307 28.56 - 57.12: 598 57.12 - 85.69: 108 85.69 - 114.25: 5 114.25 - 142.81: 1 Dihedral angle restraints: 11019 sinusoidal: 6425 harmonic: 4594 Sorted by residual: dihedral pdb=" CD ARG B 176 " pdb=" NE ARG B 176 " pdb=" CZ ARG B 176 " pdb=" NH1 ARG B 176 " ideal model delta sinusoidal sigma weight residual 0.00 41.02 -41.02 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA ARG B 394 " pdb=" C ARG B 394 " pdb=" N TYR B 395 " pdb=" CA TYR B 395 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" C7 A0I B 601 " pdb=" C8 A0I B 601 " pdb=" C9 A0I B 601 " pdb=" O3 A0I B 601 " ideal model delta sinusoidal sigma weight residual -91.68 51.13 -142.81 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 11016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1699 0.054 - 0.108: 161 0.108 - 0.161: 38 0.161 - 0.215: 2 0.215 - 0.269: 1 Chirality restraints: 1901 Sorted by residual: chirality pdb=" C6 A0I B 601 " pdb=" C5 A0I B 601 " pdb=" C7 A0I B 601 " pdb=" O13 A0I B 601 " both_signs ideal model delta sigma weight residual False -2.45 -2.72 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C8 A0I B 601 " pdb=" C7 A0I B 601 " pdb=" C9 A0I B 601 " pdb=" O2 A0I B 601 " both_signs ideal model delta sigma weight residual False -2.65 -2.44 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C7 A0I B 601 " pdb=" C6 A0I B 601 " pdb=" C8 A0I B 601 " pdb=" O12 A0I B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 1898 not shown) Planarity restraints: 3274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 176 " 0.749 9.50e-02 1.11e+02 2.50e-01 6.59e+01 pdb=" NE ARG B 176 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 176 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 176 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 176 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 176 " -0.012 2.00e-02 2.50e+03 pdb="HH12 ARG B 176 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG B 176 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG B 176 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 3 " -0.022 2.00e-02 2.50e+03 9.08e-03 2.68e+00 pdb=" N9 A V 3 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A V 3 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 3 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A V 3 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A V 3 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 3 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A V 3 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A V 3 " 0.002 2.00e-02 2.50e+03 pdb=" H2 A V 3 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO B 162 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.019 5.00e-02 4.00e+02 ... (remaining 3271 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 940 2.16 - 2.77: 43094 2.77 - 3.38: 65939 3.38 - 3.99: 89373 3.99 - 4.60: 135418 Nonbonded interactions: 334764 Sorted by model distance: nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.549 1.850 nonbonded pdb=" H GLY A 239 " pdb=" O ALA A 251 " model vdw 1.582 1.850 nonbonded pdb=" OD1 ASN B 397 " pdb=" HG1 THR B 399 " model vdw 1.590 1.850 nonbonded pdb=" H GLY C 85 " pdb=" OD1 ASP C 110 " model vdw 1.630 1.850 nonbonded pdb=" HG1 THR B 103 " pdb=" O ILE B 125 " model vdw 1.631 1.850 ... (remaining 334759 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 'D' and resid 5 through 17) selection = (chain 'S' and (resid 28 through 34 or resid 36 through 40)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.340 Extract box with map and model: 6.530 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 91.620 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 : 0.005 0.229 12142 Z= 0.303 Angle : 0.528 11.269 16666 Z= 0.264 Chirality : 0.037 0.269 1901 Planarity : 0.008 0.321 1951 Dihedral : 17.935 142.809 4843 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.06 % Allowed : 16.38 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1351 helix: 1.65 (0.23), residues: 525 sheet: 0.20 (0.40), residues: 148 loop : -0.07 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 44 TYR 0.012 0.001 TYR C 315 ARG 0.007 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.740 Fit side-chains revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8594 (mttt) cc_final: 0.8364 (mttp) REVERT: A 332 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7873 (mtp180) REVERT: B 282 ASP cc_start: 0.8477 (p0) cc_final: 0.8276 (p0) REVERT: B 480 GLU cc_start: 0.7593 (tt0) cc_final: 0.7385 (tt0) REVERT: C 77 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8663 (ptt90) REVERT: C 89 GLU cc_start: 0.7603 (mp0) cc_final: 0.7392 (mp0) REVERT: C 109 GLN cc_start: 0.7321 (mm-40) cc_final: 0.7065 (mp10) REVERT: C 348 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7638 (mppt) REVERT: C 351 ILE cc_start: 0.7809 (mm) cc_final: 0.7532 (mm) REVERT: C 413 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7524 (mtmt) REVERT: C 427 LYS cc_start: 0.7300 (ttmt) cc_final: 0.7088 (tttm) outliers start: 24 outliers final: 9 residues processed: 194 average time/residue: 3.6254 time to fit residues: 746.9153 Evaluate side-chains 128 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12142 Z= 0.314 Angle : 0.544 5.668 16666 Z= 0.285 Chirality : 0.039 0.133 1901 Planarity : 0.005 0.087 1951 Dihedral : 13.673 117.384 2287 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.40 % Allowed : 15.61 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1351 helix: 1.49 (0.23), residues: 526 sheet: -0.05 (0.40), residues: 138 loop : -0.09 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 346 HIS 0.005 0.001 HIS A 371 PHE 0.017 0.002 PHE C 44 TYR 0.017 0.002 TYR A 403 ARG 0.004 0.001 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 1.795 Fit side-chains revert: symmetry clash REVERT: B 53 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7485 (pptt) REVERT: C 109 GLN cc_start: 0.7323 (mm-40) cc_final: 0.7035 (mp10) REVERT: C 351 ILE cc_start: 0.7885 (mm) cc_final: 0.7614 (mm) REVERT: C 413 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7575 (mtmt) outliers start: 28 outliers final: 14 residues processed: 145 average time/residue: 3.8835 time to fit residues: 596.2401 Evaluate side-chains 133 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.8754 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12142 Z= 0.183 Angle : 0.480 5.475 16666 Z= 0.249 Chirality : 0.037 0.130 1901 Planarity : 0.004 0.073 1951 Dihedral : 13.190 104.155 2280 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.63 % Allowed : 16.30 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1351 helix: 1.64 (0.23), residues: 519 sheet: 0.07 (0.42), residues: 131 loop : -0.07 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.011 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.005 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7352 (pptt) REVERT: C 109 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7122 (mp10) REVERT: C 196 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6207 (mt-10) REVERT: C 351 ILE cc_start: 0.7852 (mm) cc_final: 0.7604 (mm) outliers start: 19 outliers final: 11 residues processed: 137 average time/residue: 3.7404 time to fit residues: 543.7402 Evaluate side-chains 130 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 133 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8742 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12142 Z= 0.164 Angle : 0.462 5.498 16666 Z= 0.239 Chirality : 0.036 0.129 1901 Planarity : 0.004 0.061 1951 Dihedral : 12.883 84.715 2278 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.29 % Allowed : 16.64 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.23), residues: 1351 helix: 1.75 (0.23), residues: 518 sheet: 0.13 (0.42), residues: 131 loop : -0.01 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.007 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.764 Fit side-chains revert: symmetry clash REVERT: C 109 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7144 (mp10) REVERT: C 196 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6193 (mt-10) REVERT: C 351 ILE cc_start: 0.7826 (mm) cc_final: 0.7593 (mm) outliers start: 15 outliers final: 11 residues processed: 132 average time/residue: 3.6258 time to fit residues: 511.1126 Evaluate side-chains 130 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 0.0570 chunk 113 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- 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: 0.8758 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12142 Z= 0.217 Angle : 0.488 5.610 16666 Z= 0.255 Chirality : 0.037 0.129 1901 Planarity : 0.004 0.058 1951 Dihedral : 12.810 73.596 2274 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.37 % Allowed : 16.30 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1351 helix: 1.68 (0.23), residues: 517 sheet: -0.04 (0.42), residues: 133 loop : -0.03 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.014 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.004 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7504 (pptt) REVERT: C 109 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7153 (mp10) REVERT: C 196 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6202 (mt-10) REVERT: C 351 ILE cc_start: 0.7796 (mm) cc_final: 0.7571 (mm) outliers start: 16 outliers final: 12 residues processed: 133 average time/residue: 3.6896 time to fit residues: 521.1611 Evaluate side-chains 130 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 78 optimal weight: 0.0070 chunk 32 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12142 Z= 0.146 Angle : 0.452 5.476 16666 Z= 0.234 Chirality : 0.036 0.129 1901 Planarity : 0.004 0.072 1951 Dihedral : 12.657 73.564 2273 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.54 % Allowed : 16.38 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1351 helix: 1.81 (0.23), residues: 518 sheet: 0.13 (0.42), residues: 131 loop : 0.01 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.009 0.001 PHE C 175 TYR 0.011 0.001 TYR A 403 ARG 0.005 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.630 Fit side-chains revert: symmetry clash REVERT: B 159 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8835 (mt) REVERT: C 109 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7148 (mp10) REVERT: C 351 ILE cc_start: 0.7781 (mm) cc_final: 0.7567 (mm) outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 3.6298 time to fit residues: 507.0194 Evaluate side-chains 125 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 97 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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: 0.8727 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12142 Z= 0.139 Angle : 0.445 5.411 16666 Z= 0.229 Chirality : 0.036 0.129 1901 Planarity : 0.004 0.072 1951 Dihedral : 12.565 73.535 2273 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.20 % Allowed : 16.90 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1351 helix: 1.93 (0.23), residues: 516 sheet: 0.21 (0.43), residues: 131 loop : 0.04 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.010 0.001 PHE C 161 TYR 0.011 0.001 TYR A 403 ARG 0.007 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.786 Fit side-chains revert: symmetry clash REVERT: B 159 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.8829 (mt) REVERT: C 109 GLN cc_start: 0.7401 (mm-40) cc_final: 0.7139 (mp10) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 3.9081 time to fit residues: 507.6434 Evaluate side-chains 123 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.8769 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12142 Z= 0.286 Angle : 0.520 5.735 16666 Z= 0.272 Chirality : 0.038 0.130 1901 Planarity : 0.005 0.077 1951 Dihedral : 12.761 73.589 2273 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.37 % Allowed : 16.81 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1351 helix: 1.64 (0.23), residues: 518 sheet: -0.03 (0.41), residues: 138 loop : -0.03 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 346 HIS 0.005 0.001 HIS A 371 PHE 0.018 0.002 PHE C 44 TYR 0.016 0.002 TYR A 403 ARG 0.006 0.001 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.909 Fit side-chains revert: symmetry clash REVERT: C 109 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7130 (mp10) outliers start: 16 outliers final: 13 residues processed: 127 average time/residue: 3.8288 time to fit residues: 517.7947 Evaluate side-chains 122 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 3.9990 chunk 116 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 131 optimal weight: 0.3980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.8748 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12142 Z= 0.184 Angle : 0.473 5.552 16666 Z= 0.245 Chirality : 0.036 0.130 1901 Planarity : 0.004 0.074 1951 Dihedral : 12.685 73.567 2273 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.20 % Allowed : 16.81 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1351 helix: 1.73 (0.23), residues: 518 sheet: 0.00 (0.42), residues: 133 loop : 0.01 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.011 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.008 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.868 Fit side-chains revert: symmetry clash REVERT: C 109 GLN cc_start: 0.7411 (mm-40) cc_final: 0.7133 (mp10) outliers start: 14 outliers final: 13 residues processed: 126 average time/residue: 3.8347 time to fit residues: 512.8119 Evaluate side-chains 125 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.0050 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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: 0.8749 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12142 Z= 0.189 Angle : 0.476 5.444 16666 Z= 0.247 Chirality : 0.036 0.129 1901 Planarity : 0.004 0.072 1951 Dihedral : 12.655 73.571 2272 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.46 % Allowed : 16.72 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1351 helix: 1.75 (0.23), residues: 518 sheet: -0.05 (0.42), residues: 133 loop : 0.01 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.012 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.009 0.000 ARG C 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.634 Fit side-chains REVERT: C 28 HIS cc_start: 0.6146 (OUTLIER) cc_final: 0.5823 (t-90) REVERT: C 109 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7140 (mp10) outliers start: 17 outliers final: 14 residues processed: 127 average time/residue: 3.8541 time to fit residues: 520.5778 Evaluate side-chains 127 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 20 optimal weight: 0.0040 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.117371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.087048 restraints weight = 52948.457| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.80 r_work: 0.2830 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12142 Z= 0.132 Angle : 0.446 5.213 16666 Z= 0.230 Chirality : 0.035 0.130 1901 Planarity : 0.004 0.072 1951 Dihedral : 12.502 73.552 2272 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.94 % Allowed : 17.32 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1351 helix: 1.93 (0.23), residues: 518 sheet: 0.18 (0.42), residues: 129 loop : 0.05 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.008 0.001 PHE C 175 TYR 0.009 0.001 TYR A 403 ARG 0.013 0.000 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10097.28 seconds wall clock time: 176 minutes 29.35 seconds (10589.35 seconds total)