Starting phenix.real_space_refine on Thu Apr 11 09:22:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psn_17857/04_2024/8psn_17857_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psn_17857/04_2024/8psn_17857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psn_17857/04_2024/8psn_17857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psn_17857/04_2024/8psn_17857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psn_17857/04_2024/8psn_17857_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psn_17857/04_2024/8psn_17857_trim_updated.pdb" } resolution = 2.73 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= 0.003 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 31 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 7004 2.51 5 N 1995 2.21 5 O 2202 1.98 5 H 10965 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 396": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22266 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6651 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 7973 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} Chain: "C" Number of atoms: 6714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 6714 Classifications: {'peptide': 429} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 406} 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': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "S" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 486 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CTP': 1} Classifications: {'undetermined': 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2584 SG CYS A 161 54.626 54.626 106.057 1.00 39.15 S ATOM 4472 SG CYS A 282 53.091 56.918 108.861 1.00 41.12 S ATOM 18270 SG CYS C 233 21.302 50.756 19.577 1.00 58.83 S ATOM 18294 SG CYS C 235 21.162 49.313 23.166 1.00 50.34 S ATOM 16936 SG CYS C 146 9.377 44.286 40.307 1.00 70.66 S ATOM 17124 SG CYS C 159 9.121 40.913 38.498 1.00 67.27 S ATOM 17180 SG CYS C 163 12.142 43.135 38.007 1.00 61.34 S ATOM 17190 SG CYS C 164 11.578 41.277 41.302 1.00 62.59 S Time building chain proxies: 10.35, per 1000 atoms: 0.46 Number of scatterers: 22266 At special positions: 0 Unit cell: (95.76, 105.84, 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 64 16.00 P 31 15.00 Mg 2 11.99 O 2202 8.00 N 1995 7.00 C 7004 6.00 H 10965 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: 17.97 Conformation dependent library (CDL) restraints added in 2.2 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 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " Number of angles added : 9 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 12 sheets defined 35.6% alpha, 11.2% beta 4 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 12.53 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 4.456A pdb=" N GLN A 7 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 13 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 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 237 removed outlier: 3.822A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 313 through 323 removed outlier: 4.325A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 360 through 372 Processing helix chain 'A' and resid 383 through 386 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 24 through 38 Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.710A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 182 removed outlier: 3.751A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 205 removed outlier: 3.541A pdb=" N GLN B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER B 205 " --> pdb=" O GLN B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 236 through 247 removed outlier: 3.518A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.759A 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 355 through 371 removed outlier: 3.721A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) 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 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 443 through 454 removed outlier: 3.757A pdb=" N LYS B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 496 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 removed outlier: 3.548A pdb=" N HIS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR C 23 " --> pdb=" O TYR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 53 removed outlier: 5.719A pdb=" N SER C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N CYS C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N PHE C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 6.525A 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 108 Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.577A pdb=" N VAL C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) 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 289 removed outlier: 3.578A pdb=" N VAL C 289 " --> pdb=" O GLN C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 317 removed outlier: 4.011A pdb=" N ARG C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 333 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: 6.077A pdb=" N VAL A 69 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU A 56 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 5.793A 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: 10.428A pdb=" N TRP A 198 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA A 251 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLN A 200 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N TYR A 202 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET A 255 " --> pdb=" O TYR A 202 " (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 80 Processing sheet with id= E, first strand: chain 'B' and resid 155 through 159 removed outlier: 3.767A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS B 250 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N CYS B 142 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU B 252 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N LEU B 144 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 321 through 323 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 80 Processing sheet with id= I, first strand: chain 'C' and resid 191 through 194 removed outlier: 3.648A pdb=" N CYS C 259 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL C 264 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ALA C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.560A pdb=" N VAL C 221 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N SER C 203 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LYS C 223 " --> pdb=" O SER C 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 360 through 363 Processing sheet with id= L, first strand: chain 'C' and resid 405 through 409 removed outlier: 3.607A pdb=" N SER C 388 " --> pdb=" O MET C 415 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 417 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL C 386 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N SER C 419 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL C 384 " --> pdb=" O SER C 419 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 8.74 Time building geometry restraints manager: 18.76 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: 10933 1.03 - 1.23: 47 1.23 - 1.42: 4879 1.42 - 1.62: 6605 1.62 - 1.81: 88 Bond restraints: 22552 Sorted by residual: bond pdb=" N ILE B 443 " pdb=" CA ILE B 443 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.29e+00 bond pdb=" N THR B 442 " pdb=" CA THR B 442 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.31e-02 5.83e+03 7.48e+00 bond pdb=" N THR B 442 " pdb=" H THR B 442 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.26e+00 bond pdb=" N SER C 356 " pdb=" H SER C 356 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.26e+00 bond pdb=" N SER A 269 " pdb=" H SER A 269 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.24e+00 ... (remaining 22547 not shown) Histogram of bond angle deviations from ideal: 94.85 - 102.80: 80 102.80 - 110.76: 23713 110.76 - 118.71: 7171 118.71 - 126.67: 9533 126.67 - 134.62: 227 Bond angle restraints: 40724 Sorted by residual: angle pdb=" C THR A 267 " pdb=" CA THR A 267 " pdb=" CB THR A 267 " ideal model delta sigma weight residual 110.42 120.60 -10.18 1.99e+00 2.53e-01 2.62e+01 angle pdb=" PA CTP E 1 " pdb=" O3A CTP E 1 " pdb=" PB CTP E 1 " ideal model delta sigma weight residual 120.50 134.62 -14.12 3.00e+00 1.11e-01 2.22e+01 angle pdb=" N PRO A 61 " pdb=" CD PRO A 61 " pdb=" CG PRO A 61 " ideal model delta sigma weight residual 103.20 97.23 5.97 1.50e+00 4.44e-01 1.59e+01 angle pdb=" C2' CTP E 1 " pdb=" C3' CTP E 1 " pdb=" C4' CTP E 1 " ideal model delta sigma weight residual 111.00 99.73 11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" PB CTP E 1 " pdb=" O3B CTP E 1 " pdb=" PG CTP E 1 " ideal model delta sigma weight residual 120.50 131.71 -11.21 3.00e+00 1.11e-01 1.40e+01 ... (remaining 40719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 10108 33.70 - 67.41: 500 67.41 - 101.11: 24 101.11 - 134.81: 5 134.81 - 168.51: 4 Dihedral angle restraints: 10641 sinusoidal: 6042 harmonic: 4599 Sorted by residual: dihedral pdb=" O3B CTP E 1 " pdb=" O3A CTP E 1 " pdb=" PB CTP E 1 " pdb=" PA CTP E 1 " ideal model delta sinusoidal sigma weight residual 320.71 161.43 159.28 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O1G CTP E 1 " pdb=" O3B CTP E 1 " pdb=" PG CTP E 1 " pdb=" PB CTP E 1 " ideal model delta sinusoidal sigma weight residual 82.72 -44.76 127.48 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" O3A CTP E 1 " pdb=" O3B CTP E 1 " pdb=" PB CTP E 1 " pdb=" PG CTP E 1 " ideal model delta sinusoidal sigma weight residual -155.50 -51.90 -103.60 1 2.00e+01 2.50e-03 2.96e+01 ... (remaining 10638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1575 0.051 - 0.102: 160 0.102 - 0.153: 43 0.153 - 0.204: 1 0.204 - 0.254: 1 Chirality restraints: 1780 Sorted by residual: chirality pdb=" C2' CTP E 1 " pdb=" C1' CTP E 1 " pdb=" C3' CTP E 1 " pdb=" O2' CTP E 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ILE B 443 " pdb=" N ILE B 443 " pdb=" C ILE B 443 " pdb=" CB ILE B 443 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" C3' G S 1 " pdb=" C4' G S 1 " pdb=" O3' G S 1 " pdb=" C2' G S 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.61 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 1777 not shown) Planarity restraints: 3244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 445 " 0.099 2.00e-02 2.50e+03 1.06e-01 1.68e+02 pdb=" CD GLN B 445 " -0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN B 445 " -0.095 2.00e-02 2.50e+03 pdb=" NE2 GLN B 445 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 445 " -0.154 2.00e-02 2.50e+03 pdb="HE22 GLN B 445 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 268 " -0.012 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" N SER A 269 " 0.038 2.00e-02 2.50e+03 pdb=" CA SER A 269 " -0.010 2.00e-02 2.50e+03 pdb=" H SER A 269 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 265 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C ARG A 265 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG A 265 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO A 266 " 0.012 2.00e-02 2.50e+03 ... (remaining 3241 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 817 2.15 - 2.76: 41240 2.76 - 3.37: 63081 3.37 - 3.99: 83834 3.99 - 4.60: 129946 Nonbonded interactions: 318918 Sorted by model distance: nonbonded pdb=" OD2 ASP B 467 " pdb=" HE ARG B 490 " model vdw 1.535 1.850 nonbonded pdb=" H GLY C 85 " pdb=" OD1 ASP C 110 " model vdw 1.556 1.850 nonbonded pdb=" O THR C 319 " pdb=" H ARG C 323 " model vdw 1.615 1.850 nonbonded pdb=" O LEU B 179 " pdb=" HG SER B 183 " model vdw 1.618 1.850 nonbonded pdb=" OD2 ASP B 222 " pdb="HH22 ARG B 247 " model vdw 1.632 1.850 ... (remaining 318913 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.320 Extract box with map and model: 6.670 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 88.760 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 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 : 0.003 0.049 11587 Z= 0.176 Angle : 0.574 14.120 15800 Z= 0.296 Chirality : 0.037 0.254 1780 Planarity : 0.004 0.051 1933 Dihedral : 18.647 168.513 4511 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.79 % Rotamer: Outliers : 2.57 % Allowed : 20.53 % Favored : 76.90 % Cbeta Deviations : 0.08 % 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: 1.12 (0.23), residues: 1355 helix: 1.91 (0.24), residues: 514 sheet: -0.05 (0.45), residues: 120 loop : 0.10 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 175 TYR 0.009 0.001 TYR A 403 ARG 0.002 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8048 (mm) cc_final: 0.7752 (mp) outliers start: 30 outliers final: 27 residues processed: 154 average time/residue: 3.1760 time to fit residues: 523.9286 Evaluate side-chains 139 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 385 THR 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: 1.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 106 optimal weight: 0.0070 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11587 Z= 0.195 Angle : 0.492 6.570 15800 Z= 0.252 Chirality : 0.037 0.138 1780 Planarity : 0.004 0.050 1933 Dihedral : 13.193 168.479 1960 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 2.40 % Allowed : 20.53 % Favored : 77.07 % 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: 1355 helix: 1.73 (0.23), residues: 513 sheet: -0.16 (0.45), residues: 120 loop : 0.04 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.013 0.001 TYR A 403 ARG 0.003 0.000 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 1.881 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7986 (mm) cc_final: 0.7749 (mp) REVERT: C 396 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7281 (mm-30) outliers start: 28 outliers final: 20 residues processed: 144 average time/residue: 3.2088 time to fit residues: 497.5839 Evaluate side-chains 133 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 385 THR 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: 2.9990 chunk 102 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11587 Z= 0.200 Angle : 0.487 7.147 15800 Z= 0.251 Chirality : 0.037 0.135 1780 Planarity : 0.004 0.049 1933 Dihedral : 12.747 167.531 1940 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.71 % Rotamer: Outliers : 2.48 % Allowed : 20.79 % Favored : 76.73 % 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: 0.86 (0.22), residues: 1355 helix: 1.62 (0.23), residues: 513 sheet: -0.19 (0.45), residues: 120 loop : 0.01 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.013 0.001 TYR A 403 ARG 0.003 0.000 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.830 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7992 (mm) cc_final: 0.7763 (mp) REVERT: C 124 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7603 (t0) REVERT: C 396 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7275 (mm-30) outliers start: 29 outliers final: 16 residues processed: 138 average time/residue: 3.1615 time to fit residues: 468.2554 Evaluate side-chains 130 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 87 GLN A 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11587 Z= 0.305 Angle : 0.539 7.644 15800 Z= 0.281 Chirality : 0.040 0.140 1780 Planarity : 0.005 0.049 1933 Dihedral : 12.956 164.745 1933 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.58 % Favored : 97.34 % Rotamer: Outliers : 3.17 % Allowed : 19.93 % Favored : 76.90 % 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: 0.65 (0.22), residues: 1355 helix: 1.42 (0.23), residues: 509 sheet: -0.25 (0.44), residues: 120 loop : -0.08 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 263 HIS 0.006 0.001 HIS B 174 PHE 0.013 0.002 PHE B 287 TYR 0.015 0.001 TYR A 403 ARG 0.003 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7980 (mm) cc_final: 0.7773 (mp) REVERT: A 85 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: A 119 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7537 (mtp180) REVERT: C 396 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7274 (mm-30) outliers start: 37 outliers final: 21 residues processed: 145 average time/residue: 3.2131 time to fit residues: 498.9611 Evaluate side-chains 133 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 87 GLN A 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11587 Z= 0.278 Angle : 0.528 7.491 15800 Z= 0.274 Chirality : 0.039 0.142 1780 Planarity : 0.005 0.050 1933 Dihedral : 12.971 164.027 1933 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.71 % Rotamer: Outliers : 2.65 % Allowed : 20.36 % Favored : 76.99 % 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: 0.57 (0.22), residues: 1355 helix: 1.36 (0.23), residues: 509 sheet: -0.30 (0.44), residues: 120 loop : -0.14 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.013 0.002 PHE B 287 TYR 0.014 0.001 TYR A 403 ARG 0.005 0.000 ARG C 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7051 (tt0) REVERT: C 124 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7596 (t0) REVERT: C 396 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7295 (mm-30) outliers start: 31 outliers final: 22 residues processed: 141 average time/residue: 3.1058 time to fit residues: 471.3866 Evaluate side-chains 133 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 0.3980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11587 Z= 0.230 Angle : 0.506 7.171 15800 Z= 0.263 Chirality : 0.038 0.137 1780 Planarity : 0.005 0.048 1933 Dihedral : 12.868 164.028 1932 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.44 % Favored : 97.49 % Rotamer: Outliers : 2.82 % Allowed : 20.53 % Favored : 76.65 % 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: 0.62 (0.22), residues: 1355 helix: 1.42 (0.23), residues: 509 sheet: -0.33 (0.44), residues: 120 loop : -0.12 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.012 0.001 PHE B 287 TYR 0.013 0.001 TYR A 403 ARG 0.006 0.000 ARG C 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: C 124 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7575 (t0) REVERT: C 396 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7353 (mm-30) outliers start: 33 outliers final: 23 residues processed: 139 average time/residue: 3.2867 time to fit residues: 489.0653 Evaluate side-chains 132 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.8683 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11587 Z= 0.216 Angle : 0.499 7.190 15800 Z= 0.259 Chirality : 0.038 0.136 1780 Planarity : 0.005 0.055 1933 Dihedral : 12.839 164.326 1932 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 2.99 % Allowed : 20.02 % Favored : 76.99 % 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: 0.67 (0.22), residues: 1355 helix: 1.46 (0.23), residues: 509 sheet: -0.15 (0.45), residues: 116 loop : -0.12 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE B 287 TYR 0.013 0.001 TYR A 403 ARG 0.009 0.000 ARG C 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7069 (tt0) REVERT: C 124 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7540 (t0) REVERT: C 396 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7342 (mm-30) outliers start: 35 outliers final: 27 residues processed: 141 average time/residue: 3.3673 time to fit residues: 512.6998 Evaluate side-chains 137 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8675 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11587 Z= 0.185 Angle : 0.483 7.002 15800 Z= 0.250 Chirality : 0.037 0.134 1780 Planarity : 0.004 0.057 1933 Dihedral : 12.747 164.604 1931 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.79 % Rotamer: Outliers : 3.08 % Allowed : 20.02 % Favored : 76.90 % 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: 0.75 (0.22), residues: 1355 helix: 1.54 (0.23), residues: 509 sheet: -0.32 (0.44), residues: 120 loop : -0.04 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.009 0.000 ARG C 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: C 124 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7524 (t0) REVERT: C 396 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7312 (mm-30) outliers start: 36 outliers final: 28 residues processed: 141 average time/residue: 3.2070 time to fit residues: 484.6207 Evaluate side-chains 138 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8676 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11587 Z= 0.189 Angle : 0.486 7.072 15800 Z= 0.251 Chirality : 0.037 0.134 1780 Planarity : 0.005 0.060 1933 Dihedral : 12.721 164.596 1931 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 2.91 % Allowed : 20.36 % Favored : 76.73 % 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: 0.78 (0.22), residues: 1355 helix: 1.54 (0.23), residues: 509 sheet: -0.32 (0.44), residues: 120 loop : 0.00 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.008 0.000 ARG C 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: C 124 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7514 (t0) REVERT: C 396 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7310 (mm-30) outliers start: 34 outliers final: 28 residues processed: 139 average time/residue: 3.0614 time to fit residues: 457.3869 Evaluate side-chains 137 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11587 Z= 0.181 Angle : 0.480 6.961 15800 Z= 0.248 Chirality : 0.037 0.133 1780 Planarity : 0.004 0.049 1933 Dihedral : 12.673 164.613 1931 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.93 % Rotamer: Outliers : 2.65 % Allowed : 20.62 % Favored : 76.73 % 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: 0.80 (0.23), residues: 1355 helix: 1.57 (0.24), residues: 509 sheet: -0.32 (0.44), residues: 120 loop : 0.01 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.004 0.000 ARG A 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: C 124 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7505 (t0) REVERT: C 396 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7310 (mm-30) outliers start: 31 outliers final: 26 residues processed: 133 average time/residue: 3.2977 time to fit residues: 469.5676 Evaluate side-chains 134 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.3980 chunk 99 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.118776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.097303 restraints weight = 37396.734| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.24 r_work: 0.2886 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11587 Z= 0.174 Angle : 0.478 6.886 15800 Z= 0.247 Chirality : 0.037 0.132 1780 Planarity : 0.005 0.072 1933 Dihedral : 12.634 164.602 1931 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.79 % Rotamer: Outliers : 2.57 % Allowed : 20.87 % Favored : 76.56 % 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: 0.84 (0.23), residues: 1355 helix: 1.60 (0.24), residues: 509 sheet: -0.30 (0.44), residues: 120 loop : 0.03 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.009 0.000 ARG C 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8910.43 seconds wall clock time: 158 minutes 11.23 seconds (9491.23 seconds total)