Starting phenix.real_space_refine on Mon Mar 18 22:47:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/03_2024/8psx_17864_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/03_2024/8psx_17864.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/03_2024/8psx_17864_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/03_2024/8psx_17864_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/03_2024/8psx_17864_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/03_2024/8psx_17864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/03_2024/8psx_17864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/03_2024/8psx_17864_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/03_2024/8psx_17864_trim_updated.pdb" } resolution = 2.96 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 37 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 7046 2.51 5 N 2010 2.21 5 O 2239 1.98 5 H 11003 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22403 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6652 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: 6676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6676 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 22, 'TRANS': 403} 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: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 250 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 3} 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 45.999 46.033 18.402 1.00 25.04 S ATOM 4473 SG CYS A 282 43.659 44.596 15.566 1.00 19.11 S ATOM 18214 SG CYS C 233 23.303 55.910 108.964 1.00 84.75 S ATOM 18238 SG CYS C 235 23.645 57.568 105.415 1.00 85.78 S ATOM 16880 SG CYS C 146 12.277 64.309 89.727 1.00 78.45 S ATOM 17068 SG CYS C 159 11.918 67.914 91.277 1.00 82.86 S ATOM 17124 SG CYS C 163 14.801 65.538 91.727 1.00 75.36 S ATOM 17134 SG CYS C 164 14.321 67.369 88.371 1.00 76.72 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: 13.54, per 1000 atoms: 0.60 Number of scatterers: 22403 At special positions: 0 Unit cell: (91.56, 103.32, 126, 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 37 15.00 Mg 2 11.99 O 2239 8.00 N 2010 7.00 C 7046 6.00 H 11003 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: 19.04 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=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " 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 163 " 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 164 " Number of angles added : 8 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 11 sheets defined 35.7% alpha, 10.5% beta 9 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 13.02 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 4.667A pdb=" N GLN A 7 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.802A pdb=" N LYS A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 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: 3.690A 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: 4.422A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 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 39 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 138 removed outlier: 3.769A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 182 removed outlier: 3.525A 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 removed outlier: 3.575A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.702A 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 434 removed outlier: 3.985A 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 496 Processing helix chain 'B' and resid 507 through 514 Processing helix chain 'C' and resid 3 through 7 removed outlier: 3.788A pdb=" N SER C 7 " --> pdb=" O PHE C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 34 through 53 removed outlier: 5.817A pdb=" N SER C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N PHE C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N PHE C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 6.471A 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 106 Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 209 through 218 Processing helix chain 'C' and resid 234 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: 5.999A pdb=" N VAL A 69 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU A 56 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.066A 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: 7.365A pdb=" N ALA A 251 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLN A 200 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N TYR A 202 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET A 255 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 74 through 80 Processing sheet with id= D, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.574A pdb=" N CYS B 250 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N CYS B 142 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU B 252 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LEU B 144 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 209 through 211 Processing sheet with id= F, first strand: chain 'B' and resid 326 through 329 Processing sheet with id= G, first strand: chain 'C' and resid 77 through 83 Processing sheet with id= H, first strand: chain 'C' and resid 191 through 194 removed outlier: 3.761A pdb=" N CYS C 259 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL C 264 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.724A pdb=" N VAL C 221 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N SER C 203 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYS C 223 " --> pdb=" O SER C 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= I 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: 3.549A pdb=" N SER C 388 " --> pdb=" O MET C 415 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 417 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL C 386 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER C 419 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL C 384 " --> pdb=" O SER C 419 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 982 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 8.55 Time building geometry restraints manager: 19.70 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: 10971 1.03 - 1.23: 49 1.23 - 1.42: 4962 1.42 - 1.62: 6634 1.62 - 1.81: 89 Bond restraints: 22705 Sorted by residual: bond pdb=" C6 A0I B 601 " pdb=" C7 A0I B 601 " ideal model delta sigma weight residual 1.302 1.530 -0.228 2.00e-02 2.50e+03 1.30e+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 5.76e+01 bond pdb=" C4 A0I B 601 " pdb=" N3 A0I B 601 " ideal model delta sigma weight residual 1.475 1.325 0.150 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 1.354 0.145 2.00e-02 2.50e+03 5.28e+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 3.24e+01 ... (remaining 22700 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.14: 442 106.14 - 113.09: 26327 113.09 - 120.05: 6975 120.05 - 127.01: 7052 127.01 - 133.97: 199 Bond angle restraints: 40995 Sorted by residual: angle pdb=" C LYS A 163 " pdb=" CA LYS A 163 " pdb=" CB LYS A 163 " ideal model delta sigma weight residual 116.54 111.92 4.62 1.15e+00 7.56e-01 1.61e+01 angle pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" CD PRO A 132 " ideal model delta sigma weight residual 112.00 106.90 5.10 1.40e+00 5.10e-01 1.33e+01 angle pdb=" P1 A0I B 601 " pdb=" N4 A0I B 601 " pdb=" P2 A0I B 601 " ideal model delta sigma weight residual 120.05 130.22 -10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" P2 A0I B 601 " pdb=" O7 A0I B 601 " pdb=" P3 A0I B 601 " ideal model delta sigma weight residual 123.66 133.31 -9.65 3.00e+00 1.11e-01 1.03e+01 angle pdb=" O5 A0I B 601 " pdb=" P2 A0I B 601 " pdb=" O6 A0I B 601 " ideal model delta sigma weight residual 109.46 118.77 -9.31 3.00e+00 1.11e-01 9.63e+00 ... (remaining 40990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.40: 10036 28.40 - 56.81: 574 56.81 - 85.21: 78 85.21 - 113.61: 8 113.61 - 142.02: 2 Dihedral angle restraints: 10698 sinusoidal: 6102 harmonic: 4596 Sorted by residual: 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 50.34 -142.02 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" CA ALA A 77 " pdb=" C ALA A 77 " pdb=" N THR A 78 " pdb=" CA THR A 78 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" O11 A0I B 601 " pdb=" N4 A0I B 601 " pdb=" P1 A0I B 601 " pdb=" P2 A0I B 601 " ideal model delta sinusoidal sigma weight residual 79.43 -158.89 -121.68 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 10695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1609 0.054 - 0.108: 152 0.108 - 0.162: 43 0.162 - 0.215: 2 0.215 - 0.269: 1 Chirality restraints: 1807 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 1.09e+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 -2.58 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1804 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 83 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO C 84 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 427 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C ASP B 427 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP B 427 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS B 428 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 131 " 0.033 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 132 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.027 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1964 2.21 - 2.81: 46062 2.81 - 3.41: 61012 3.41 - 4.00: 84391 4.00 - 4.60: 126542 Nonbonded interactions: 319971 Sorted by model distance: nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.618 1.850 nonbonded pdb="HH22 ARG A 201 " pdb=" O LYS A 263 " model vdw 1.622 1.850 nonbonded pdb="HE22 GLN B 57 " pdb=" OP1 U P 5 " model vdw 1.632 1.850 nonbonded pdb=" OE2 GLU B 148 " pdb=" HE ARG B 155 " model vdw 1.646 1.850 nonbonded pdb=" H TYR A 18 " pdb=" O SER A 22 " model vdw 1.653 1.850 ... (remaining 319966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.140 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: 0.350 Extract box with map and model: 6.650 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 94.540 Find NCS groups from input model: 0.430 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 0.228 11702 Z= 0.337 Angle : 0.551 10.175 15982 Z= 0.278 Chirality : 0.037 0.269 1807 Planarity : 0.004 0.114 1934 Dihedral : 17.817 142.016 4561 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.71 % Allowed : 19.19 % Favored : 79.09 % 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: 0.82 (0.23), residues: 1352 helix: 1.62 (0.23), residues: 534 sheet: -0.70 (0.37), residues: 163 loop : 0.08 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.012 0.001 PHE C 82 TYR 0.010 0.001 TYR A 403 ARG 0.002 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 151 average time/residue: 3.0114 time to fit residues: 488.5550 Evaluate side-chains 143 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 399 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11702 Z= 0.251 Angle : 0.512 5.232 15982 Z= 0.264 Chirality : 0.038 0.134 1807 Planarity : 0.004 0.070 1934 Dihedral : 11.829 136.965 2016 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.17 % Allowed : 17.82 % Favored : 79.01 % 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: 0.57 (0.23), residues: 1352 helix: 1.41 (0.23), residues: 533 sheet: -0.79 (0.36), residues: 166 loop : -0.07 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 209 HIS 0.005 0.001 HIS B 378 PHE 0.014 0.001 PHE B 4 TYR 0.013 0.001 TYR A 403 ARG 0.003 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: B 59 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7157 (pp20) REVERT: B 427 ASP cc_start: 0.7836 (t0) cc_final: 0.7311 (t0) REVERT: C 358 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: C 396 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6716 (mt-10) outliers start: 37 outliers final: 17 residues processed: 157 average time/residue: 2.8441 time to fit residues: 482.3491 Evaluate side-chains 151 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11702 Z= 0.330 Angle : 0.556 5.434 15982 Z= 0.290 Chirality : 0.040 0.138 1807 Planarity : 0.005 0.061 1934 Dihedral : 12.002 139.647 2001 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.34 % Allowed : 17.82 % Favored : 78.83 % 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: 0.23 (0.22), residues: 1352 helix: 1.11 (0.23), residues: 530 sheet: -0.82 (0.37), residues: 154 loop : -0.30 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 77 HIS 0.006 0.001 HIS B 378 PHE 0.017 0.002 PHE B 4 TYR 0.015 0.002 TYR A 403 ARG 0.004 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: B 59 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7200 (pp20) REVERT: B 427 ASP cc_start: 0.7848 (t0) cc_final: 0.7316 (t0) REVERT: B 467 ASP cc_start: 0.7603 (t0) cc_final: 0.7403 (t70) REVERT: C 115 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7231 (mm-30) REVERT: C 317 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.7009 (ptt180) REVERT: C 358 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6805 (mp0) outliers start: 39 outliers final: 25 residues processed: 161 average time/residue: 2.9933 time to fit residues: 517.4291 Evaluate side-chains 156 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 59 GLU 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 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11702 Z= 0.261 Angle : 0.514 5.058 15982 Z= 0.268 Chirality : 0.038 0.138 1807 Planarity : 0.004 0.057 1934 Dihedral : 11.866 136.520 2000 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.34 % Allowed : 17.65 % Favored : 79.01 % 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: 0.24 (0.22), residues: 1352 helix: 1.13 (0.23), residues: 531 sheet: -0.85 (0.37), residues: 154 loop : -0.30 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 77 HIS 0.004 0.001 HIS B 378 PHE 0.013 0.001 PHE B 4 TYR 0.013 0.002 TYR A 403 ARG 0.003 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: B 59 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7181 (pp20) REVERT: B 427 ASP cc_start: 0.7824 (t0) cc_final: 0.7288 (t0) REVERT: B 467 ASP cc_start: 0.7699 (t0) cc_final: 0.7448 (t70) REVERT: C 32 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6450 (mt) REVERT: C 115 GLU cc_start: 0.7518 (mm-30) cc_final: 0.6569 (mp0) REVERT: C 358 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6874 (mp0) outliers start: 39 outliers final: 27 residues processed: 159 average time/residue: 2.9664 time to fit residues: 506.2807 Evaluate side-chains 161 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11702 Z= 0.232 Angle : 0.497 4.836 15982 Z= 0.258 Chirality : 0.038 0.137 1807 Planarity : 0.004 0.053 1934 Dihedral : 11.646 129.801 2000 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.51 % Allowed : 17.14 % Favored : 79.35 % 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: 0.33 (0.22), residues: 1352 helix: 1.21 (0.23), residues: 531 sheet: -0.97 (0.37), residues: 154 loop : -0.21 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.011 0.001 PHE B 4 TYR 0.013 0.001 TYR A 403 ARG 0.003 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 136 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: A 84 GLN cc_start: 0.6020 (OUTLIER) cc_final: 0.5693 (tm-30) REVERT: B 59 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7168 (pp20) REVERT: B 427 ASP cc_start: 0.7771 (t0) cc_final: 0.7188 (t0) REVERT: B 467 ASP cc_start: 0.7680 (t0) cc_final: 0.7388 (t70) REVERT: C 32 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6289 (mt) REVERT: C 93 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6787 (m-30) REVERT: C 102 ASP cc_start: 0.7637 (m-30) cc_final: 0.7431 (m-30) REVERT: C 115 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6598 (mp0) REVERT: C 348 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7561 (mmmm) REVERT: C 358 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6796 (mp0) outliers start: 41 outliers final: 23 residues processed: 164 average time/residue: 2.9063 time to fit residues: 512.5036 Evaluate side-chains 161 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 131 optimal weight: 0.0470 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11702 Z= 0.207 Angle : 0.483 4.629 15982 Z= 0.250 Chirality : 0.037 0.137 1807 Planarity : 0.004 0.052 1934 Dihedral : 11.463 128.050 1999 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.83 % Allowed : 17.99 % Favored : 79.18 % 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: 0.43 (0.23), residues: 1352 helix: 1.31 (0.23), residues: 531 sheet: -0.91 (0.38), residues: 154 loop : -0.15 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 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 0.003 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: A 31 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8413 (m) REVERT: A 84 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5675 (tm-30) REVERT: B 306 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: B 427 ASP cc_start: 0.7765 (t0) cc_final: 0.7167 (t0) REVERT: B 467 ASP cc_start: 0.7652 (t0) cc_final: 0.7367 (t70) REVERT: C 32 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6286 (mt) REVERT: C 102 ASP cc_start: 0.7672 (m-30) cc_final: 0.7442 (m-30) REVERT: C 115 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6599 (mp0) REVERT: C 358 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6715 (mp0) outliers start: 33 outliers final: 22 residues processed: 152 average time/residue: 3.0950 time to fit residues: 504.7235 Evaluate side-chains 155 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 0.0010 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.0980 chunk 52 optimal weight: 0.1980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11702 Z= 0.131 Angle : 0.440 4.210 15982 Z= 0.225 Chirality : 0.036 0.136 1807 Planarity : 0.003 0.049 1934 Dihedral : 10.805 110.839 1996 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.89 % Allowed : 19.02 % Favored : 79.09 % 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: 0.83 (0.23), residues: 1352 helix: 1.68 (0.24), residues: 531 sheet: -0.81 (0.39), residues: 153 loop : 0.06 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.003 0.000 HIS B 174 PHE 0.007 0.001 PHE B 158 TYR 0.007 0.001 TYR A 403 ARG 0.002 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.5974 (OUTLIER) cc_final: 0.5639 (tm-30) REVERT: A 317 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.8146 (ttm170) REVERT: B 84 ARG cc_start: 0.6497 (mtm110) cc_final: 0.6247 (mtm180) REVERT: B 96 MET cc_start: 0.8956 (tpp) cc_final: 0.8402 (tpt) REVERT: B 427 ASP cc_start: 0.7753 (t0) cc_final: 0.7147 (t0) REVERT: C 102 ASP cc_start: 0.7600 (m-30) cc_final: 0.7335 (m-30) REVERT: C 358 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: C 389 ARG cc_start: 0.7248 (mmt180) cc_final: 0.6990 (mmt180) outliers start: 22 outliers final: 14 residues processed: 151 average time/residue: 3.3747 time to fit residues: 543.7863 Evaluate side-chains 146 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.0050 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 0.0970 chunk 125 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11702 Z= 0.136 Angle : 0.439 4.178 15982 Z= 0.224 Chirality : 0.036 0.135 1807 Planarity : 0.004 0.061 1934 Dihedral : 10.569 99.151 1991 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.97 % Allowed : 19.11 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.23), residues: 1352 helix: 1.77 (0.24), residues: 531 sheet: -0.73 (0.39), residues: 153 loop : 0.14 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 209 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 0.010 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.5974 (OUTLIER) cc_final: 0.5649 (tm-30) REVERT: A 317 ARG cc_start: 0.8372 (ttp-170) cc_final: 0.8161 (ttm170) REVERT: B 84 ARG cc_start: 0.6436 (mtm110) cc_final: 0.6205 (mtm180) REVERT: B 427 ASP cc_start: 0.7747 (t0) cc_final: 0.7147 (t0) REVERT: C 32 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6356 (mt) REVERT: C 267 ARG cc_start: 0.6798 (mtm180) cc_final: 0.6579 (mtm180) REVERT: C 348 LYS cc_start: 0.8038 (mmtm) cc_final: 0.7494 (mmmm) REVERT: C 358 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: C 389 ARG cc_start: 0.7240 (mmt180) cc_final: 0.6979 (mmt180) outliers start: 23 outliers final: 17 residues processed: 143 average time/residue: 3.2741 time to fit residues: 500.2673 Evaluate side-chains 148 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.0970 chunk 125 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11702 Z= 0.142 Angle : 0.439 4.201 15982 Z= 0.224 Chirality : 0.036 0.134 1807 Planarity : 0.004 0.056 1934 Dihedral : 10.423 87.777 1989 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.89 % Allowed : 19.28 % Favored : 78.83 % 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: 1352 helix: 1.78 (0.24), residues: 532 sheet: -0.73 (0.39), residues: 153 loop : 0.16 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.003 0.001 HIS B 174 PHE 0.008 0.001 PHE C 175 TYR 0.010 0.001 TYR A 403 ARG 0.008 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.935 Fit side-chains revert: symmetry clash REVERT: A 84 GLN cc_start: 0.6002 (OUTLIER) cc_final: 0.5673 (tm-30) REVERT: A 317 ARG cc_start: 0.8373 (ttp-170) cc_final: 0.8163 (ttm170) REVERT: B 84 ARG cc_start: 0.6442 (mtm110) cc_final: 0.6206 (mtm180) REVERT: B 306 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: B 427 ASP cc_start: 0.7748 (t0) cc_final: 0.7143 (t0) REVERT: C 102 ASP cc_start: 0.7512 (m-30) cc_final: 0.7286 (m-30) REVERT: C 267 ARG cc_start: 0.6758 (mtm180) cc_final: 0.6538 (mtm180) REVERT: C 348 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7479 (mmmm) REVERT: C 358 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: C 389 ARG cc_start: 0.7235 (mmt180) cc_final: 0.6969 (mmt180) outliers start: 22 outliers final: 17 residues processed: 143 average time/residue: 3.2903 time to fit residues: 505.8792 Evaluate side-chains 145 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11702 Z= 0.228 Angle : 0.487 4.511 15982 Z= 0.251 Chirality : 0.038 0.136 1807 Planarity : 0.004 0.062 1934 Dihedral : 10.626 89.148 1989 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.71 % Allowed : 19.62 % Favored : 78.66 % 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: 0.72 (0.23), residues: 1352 helix: 1.55 (0.24), residues: 531 sheet: -0.83 (0.38), residues: 158 loop : 0.03 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 77 HIS 0.006 0.001 HIS B 378 PHE 0.013 0.001 PHE B 4 TYR 0.014 0.001 TYR A 403 ARG 0.007 0.000 ARG C 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 84 GLN cc_start: 0.6029 (OUTLIER) cc_final: 0.5694 (tm-30) REVERT: B 84 ARG cc_start: 0.6483 (mtm110) cc_final: 0.6193 (mtm180) REVERT: B 88 LYS cc_start: 0.7496 (mmmt) cc_final: 0.7276 (mmmt) REVERT: B 306 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: B 427 ASP cc_start: 0.7748 (t0) cc_final: 0.7103 (t0) REVERT: C 267 ARG cc_start: 0.6768 (mtm180) cc_final: 0.6535 (mtm180) REVERT: C 358 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6665 (mp0) outliers start: 20 outliers final: 16 residues processed: 138 average time/residue: 3.3681 time to fit residues: 496.2078 Evaluate side-chains 144 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 6 optimal weight: 0.0060 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.135742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.112504 restraints weight = 56246.774| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.73 r_work: 0.3013 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11702 Z= 0.149 Angle : 0.450 4.216 15982 Z= 0.231 Chirality : 0.036 0.133 1807 Planarity : 0.004 0.070 1934 Dihedral : 10.421 80.535 1987 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.80 % Allowed : 19.54 % Favored : 78.66 % 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: 0.84 (0.23), residues: 1352 helix: 1.66 (0.24), residues: 531 sheet: -0.77 (0.39), residues: 153 loop : 0.08 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 175 TYR 0.010 0.001 TYR A 403 ARG 0.009 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8958.38 seconds wall clock time: 156 minutes 42.57 seconds (9402.57 seconds total)