Starting phenix.real_space_refine on Thu Feb 15 15:51:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe2_20321/02_2024/6pe2_20321_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe2_20321/02_2024/6pe2_20321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe2_20321/02_2024/6pe2_20321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe2_20321/02_2024/6pe2_20321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe2_20321/02_2024/6pe2_20321_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe2_20321/02_2024/6pe2_20321_updated.pdb" } resolution = 4.0 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: 6 Type Number sf(0) Gaussians P 176 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 7547 2.51 5 N 2222 2.21 5 O 2761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 261": "NH1" <-> "NH2" Residue "G PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 389": "OE1" <-> "OE2" Residue "G GLU 432": "OE1" <-> "OE2" Residue "G ARG 525": "NH1" <-> "NH2" Residue "G ARG 564": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12746 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3611 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 13, 'TRANS': 442} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 980 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 557 Classifications: {'DNA': 27} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 26} Chain: "E" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1143 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain breaks: 1 Chain: "G" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3626 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 13, 'TRANS': 442} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 62 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 980 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "J" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 416 Classifications: {'DNA': 20} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 19} Chain: "K" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 997 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.35, per 1000 atoms: 0.58 Number of scatterers: 12746 At special positions: 0 Unit cell: (126.44, 110.2, 136.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 176 15.00 Mg 4 11.99 O 2761 8.00 N 2222 7.00 C 7547 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.74 Conformation dependent library (CDL) restraints added in 1.7 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 6 sheets defined 51.4% alpha, 7.8% beta 74 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.933A pdb=" N GLU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 173 through 182 removed outlier: 3.603A pdb=" N HIS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 198 removed outlier: 3.730A pdb=" N ASP A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 366 through 375 Processing helix chain 'A' and resid 388 through 391 No H-bonds generated for 'chain 'A' and resid 388 through 391' Processing helix chain 'A' and resid 401 through 407 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 429 through 446 Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.842A pdb=" N ASP A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 514 Processing helix chain 'A' and resid 522 through 525 Processing helix chain 'A' and resid 528 through 539 Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'B' and resid 621 through 638 Processing helix chain 'B' and resid 653 through 656 No H-bonds generated for 'chain 'B' and resid 653 through 656' Processing helix chain 'B' and resid 668 through 681 Processing helix chain 'B' and resid 694 through 701 Processing helix chain 'B' and resid 709 through 733 Processing helix chain 'G' and resid 116 through 140 removed outlier: 3.974A pdb=" N LEU G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU G 134 " --> pdb=" O SER G 130 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU G 135 " --> pdb=" O GLN G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 149 Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 174 through 183 removed outlier: 3.570A pdb=" N HIS G 179 " --> pdb=" O ARG G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 199 removed outlier: 3.665A pdb=" N ASP G 199 " --> pdb=" O ARG G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 213 Processing helix chain 'G' and resid 281 through 294 Processing helix chain 'G' and resid 307 through 315 Processing helix chain 'G' and resid 341 through 354 Processing helix chain 'G' and resid 367 through 376 Processing helix chain 'G' and resid 389 through 392 No H-bonds generated for 'chain 'G' and resid 389 through 392' Processing helix chain 'G' and resid 402 through 408 Processing helix chain 'G' and resid 411 through 422 Processing helix chain 'G' and resid 430 through 446 Processing helix chain 'G' and resid 467 through 480 removed outlier: 3.964A pdb=" N ASP G 472 " --> pdb=" O ASP G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 515 Processing helix chain 'G' and resid 523 through 525 No H-bonds generated for 'chain 'G' and resid 523 through 525' Processing helix chain 'G' and resid 529 through 540 Processing helix chain 'G' and resid 550 through 563 Processing helix chain 'G' and resid 566 through 569 removed outlier: 3.782A pdb=" N LEU G 569 " --> pdb=" O THR G 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 566 through 569' Processing helix chain 'H' and resid 621 through 638 Processing helix chain 'H' and resid 653 through 656 No H-bonds generated for 'chain 'H' and resid 653 through 656' Processing helix chain 'H' and resid 668 through 681 Processing helix chain 'H' and resid 694 through 701 Processing helix chain 'H' and resid 709 through 733 Processing sheet with id= A, first strand: chain 'A' and resid 323 through 325 removed outlier: 9.632A pdb=" N LYS A 333 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL A 298 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU A 227 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE A 300 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE A 229 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER A 302 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N GLU A 231 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL A 259 " --> pdb=" O PRO A 269 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLY A 261 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS A 267 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.818A pdb=" N ILE A 246 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 356 through 358 Processing sheet with id= D, first strand: chain 'G' and resid 324 through 326 removed outlier: 9.619A pdb=" N LYS G 334 " --> pdb=" O LEU G 297 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL G 299 " --> pdb=" O LYS G 334 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU G 228 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE G 301 " --> pdb=" O LEU G 228 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE G 230 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER G 303 " --> pdb=" O PHE G 230 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N GLU G 232 " --> pdb=" O SER G 303 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL G 260 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY G 262 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS G 268 " --> pdb=" O GLY G 262 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 240 through 242 removed outlier: 4.055A pdb=" N ILE G 247 " --> pdb=" O ASP G 242 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 357 through 359 433 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 188 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 74 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3144 1.34 - 1.45: 3386 1.45 - 1.57: 6409 1.57 - 1.69: 342 1.69 - 1.81: 56 Bond restraints: 13337 Sorted by residual: bond pdb=" N GLU G 458 " pdb=" CA GLU G 458 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.17e-02 7.31e+03 9.09e+00 bond pdb=" N ILE G 457 " pdb=" CA ILE G 457 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.29e-02 6.01e+03 7.50e+00 bond pdb=" N CYS G 456 " pdb=" CA CYS G 456 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.31e+00 bond pdb=" N ARG A 540 " pdb=" CA ARG A 540 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.06e+00 bond pdb=" C3' DG K -33 " pdb=" O3' DG K -33 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.77e+00 ... (remaining 13332 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.82: 951 105.82 - 113.22: 7446 113.22 - 120.62: 5961 120.62 - 128.02: 4137 128.02 - 135.42: 258 Bond angle restraints: 18753 Sorted by residual: angle pdb=" N CYS G 459 " pdb=" CA CYS G 459 " pdb=" C CYS G 459 " ideal model delta sigma weight residual 112.97 104.08 8.89 1.06e+00 8.90e-01 7.03e+01 angle pdb=" CA GLY A 541 " pdb=" C GLY A 541 " pdb=" O GLY A 541 " ideal model delta sigma weight residual 122.24 118.22 4.02 8.70e-01 1.32e+00 2.13e+01 angle pdb=" O3' DG K -33 " pdb=" P DC K -32 " pdb=" OP1 DC K -32 " ideal model delta sigma weight residual 108.00 118.86 -10.86 3.00e+00 1.11e-01 1.31e+01 angle pdb=" N GLU G 458 " pdb=" CA GLU G 458 " pdb=" C GLU G 458 " ideal model delta sigma weight residual 110.17 104.65 5.52 1.61e+00 3.86e-01 1.18e+01 angle pdb=" O3' DG K -33 " pdb=" P DC K -32 " pdb=" OP2 DC K -32 " ideal model delta sigma weight residual 108.00 99.16 8.84 3.00e+00 1.11e-01 8.68e+00 ... (remaining 18748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 6880 35.69 - 71.37: 634 71.37 - 107.06: 7 107.06 - 142.75: 6 142.75 - 178.44: 7 Dihedral angle restraints: 7534 sinusoidal: 4144 harmonic: 3390 Sorted by residual: dihedral pdb=" C8 GTP G 601 " pdb=" C1' GTP G 601 " pdb=" N9 GTP G 601 " pdb=" O4' GTP G 601 " ideal model delta sinusoidal sigma weight residual 104.59 -31.58 136.18 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C8 GTP A 601 " pdb=" C1' GTP A 601 " pdb=" N9 GTP A 601 " pdb=" O4' GTP A 601 " ideal model delta sinusoidal sigma weight residual 104.59 -30.62 135.21 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" CA ALA A 155 " pdb=" C ALA A 155 " pdb=" N THR A 156 " pdb=" CA THR A 156 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 7531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1797 0.049 - 0.097: 254 0.097 - 0.146: 53 0.146 - 0.194: 5 0.194 - 0.243: 1 Chirality restraints: 2110 Sorted by residual: chirality pdb=" CA CYS G 459 " pdb=" N CYS G 459 " pdb=" C CYS G 459 " pdb=" CB CYS G 459 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA MET A 537 " pdb=" N MET A 537 " pdb=" C MET A 537 " pdb=" CB MET A 537 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" P DG D 14 " pdb=" OP1 DG D 14 " pdb=" OP2 DG D 14 " pdb=" O5' DG D 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.51 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 2107 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 172 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 173 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 173 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO G 174 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 174 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 174 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 340 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 341 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.024 5.00e-02 4.00e+02 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 4 2.09 - 2.79: 2914 2.79 - 3.49: 16788 3.49 - 4.20: 33353 4.20 - 4.90: 52029 Nonbonded interactions: 105088 Sorted by model distance: nonbonded pdb=" N ALA A 235 " pdb=" CE1 HIS A 546 " model vdw 1.387 3.340 nonbonded pdb=" CA ALA A 235 " pdb=" CE1 HIS A 546 " model vdw 2.024 3.690 nonbonded pdb=" OG1 THR G 142 " pdb=" OD2 ASP G 162 " model vdw 2.062 2.440 nonbonded pdb=" O1G GTP G 601 " pdb="MG MG G 602 " model vdw 2.072 2.170 nonbonded pdb=" O1G GTP A 601 " pdb="MG MG A 602 " model vdw 2.100 2.170 ... (remaining 105083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 114 through 456 or (resid 457 and (name N or name CA or na \ me C or name O or name CB )) or resid 458 through 569 or resid 601 through 602)) \ selection = (chain 'G' and (resid 115 through 154 or (resid 155 through 156 and (name N or n \ ame CA or name C or name O or name CB )) or resid 157 through 540 or (resid 541 \ and (name N or name CA or name C or name O or name CB )) or resid 542 through 54 \ 3 or (resid 544 and (name N or name CA or name C or name O or name CB )) or resi \ d 545 or (resid 546 and (name N or name CA or name C or name O or name CB )) or \ resid 547 through 570 or resid 601 through 602)) } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = (chain 'C' and resid 1 through 9) selection = chain 'I' } ncs_group { reference = (chain 'E' and resid 20 through 74) selection = chain 'K' } 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 group one per residue 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.100 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 42.690 Find NCS groups from input model: 0.650 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 0.072 13337 Z= 0.163 Angle : 0.540 10.863 18753 Z= 0.328 Chirality : 0.036 0.243 2110 Planarity : 0.004 0.048 1783 Dihedral : 21.705 178.437 5334 Min Nonbonded Distance : 1.387 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.22), residues: 1140 helix: -0.29 (0.18), residues: 652 sheet: -0.93 (0.54), residues: 67 loop : -1.75 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 443 HIS 0.002 0.001 HIS B 681 PHE 0.008 0.001 PHE G 273 TYR 0.011 0.001 TYR G 511 ARG 0.002 0.000 ARG G 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9349 (mt) cc_final: 0.9104 (tp) REVERT: A 425 ASP cc_start: 0.8222 (p0) cc_final: 0.7997 (t0) REVERT: A 522 THR cc_start: 0.9407 (p) cc_final: 0.9194 (p) REVERT: B 647 ASN cc_start: 0.9016 (t0) cc_final: 0.8731 (t0) REVERT: B 668 PHE cc_start: 0.8504 (t80) cc_final: 0.8085 (t80) REVERT: B 693 ASN cc_start: 0.9476 (m-40) cc_final: 0.9126 (p0) REVERT: B 700 LEU cc_start: 0.9757 (tt) cc_final: 0.9462 (pp) REVERT: B 706 ASP cc_start: 0.8827 (t0) cc_final: 0.8622 (t0) REVERT: G 197 LEU cc_start: 0.9056 (mt) cc_final: 0.8790 (tt) REVERT: G 340 ASP cc_start: 0.8249 (t70) cc_final: 0.7942 (t70) REVERT: G 440 MET cc_start: 0.9352 (mmm) cc_final: 0.9066 (mmp) REVERT: H 650 PHE cc_start: 0.8727 (t80) cc_final: 0.8431 (t80) REVERT: H 668 PHE cc_start: 0.8500 (t80) cc_final: 0.8057 (t80) REVERT: H 706 ASP cc_start: 0.8293 (t0) cc_final: 0.8065 (t0) REVERT: H 718 ILE cc_start: 0.9622 (pt) cc_final: 0.9390 (mm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2637 time to fit residues: 57.9389 Evaluate side-chains 91 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 308 ASN A 399 GLN B 669 GLN B 681 HIS G 170 HIS G 309 ASN G 441 ASN G 502 ASN G 565 ASN H 669 GLN H 681 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13337 Z= 0.385 Angle : 0.668 6.875 18753 Z= 0.368 Chirality : 0.040 0.141 2110 Planarity : 0.004 0.048 1783 Dihedral : 26.308 179.496 3100 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.20 % Allowed : 9.31 % Favored : 88.49 % 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: 0.47 (0.25), residues: 1140 helix: 1.29 (0.20), residues: 650 sheet: -0.64 (0.57), residues: 54 loop : -1.04 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 443 HIS 0.006 0.001 HIS A 532 PHE 0.020 0.002 PHE A 534 TYR 0.013 0.002 TYR G 509 ARG 0.016 0.001 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.9262 (pptt) cc_final: 0.9049 (pttm) REVERT: A 476 MET cc_start: 0.9563 (mmm) cc_final: 0.9220 (mmt) REVERT: A 517 MET cc_start: 0.7891 (tpp) cc_final: 0.7544 (tpp) REVERT: A 563 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7680 (ptp90) REVERT: B 647 ASN cc_start: 0.8925 (t0) cc_final: 0.8640 (t0) REVERT: B 693 ASN cc_start: 0.9583 (m-40) cc_final: 0.9330 (p0) REVERT: G 518 MET cc_start: 0.8088 (tpt) cc_final: 0.7855 (tpp) REVERT: H 627 MET cc_start: 0.9499 (ttt) cc_final: 0.9090 (tmm) REVERT: H 650 PHE cc_start: 0.8619 (t80) cc_final: 0.8389 (t80) outliers start: 22 outliers final: 11 residues processed: 99 average time/residue: 0.2569 time to fit residues: 37.5818 Evaluate side-chains 78 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain H residue 620 ASP Chi-restraints excluded: chain H residue 670 GLU Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 ASN G 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13337 Z= 0.263 Angle : 0.567 7.932 18753 Z= 0.320 Chirality : 0.037 0.209 2110 Planarity : 0.003 0.047 1783 Dihedral : 26.223 179.124 3100 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.10 % Allowed : 10.51 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1140 helix: 1.91 (0.21), residues: 646 sheet: -0.17 (0.60), residues: 59 loop : -0.59 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 443 HIS 0.003 0.001 HIS A 342 PHE 0.018 0.001 PHE B 668 TYR 0.014 0.001 TYR B 652 ARG 0.008 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 74 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.9292 (pptt) cc_final: 0.9079 (pttt) REVERT: A 456 ILE cc_start: 0.6596 (OUTLIER) cc_final: 0.6388 (mp) REVERT: A 476 MET cc_start: 0.9497 (mmm) cc_final: 0.9281 (mmm) REVERT: A 517 MET cc_start: 0.7682 (tpp) cc_final: 0.7405 (tpp) REVERT: A 563 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7730 (ptp90) REVERT: B 627 MET cc_start: 0.9548 (ttt) cc_final: 0.9115 (tmm) REVERT: B 647 ASN cc_start: 0.8903 (t0) cc_final: 0.8668 (t0) REVERT: B 693 ASN cc_start: 0.9591 (m-40) cc_final: 0.9278 (p0) REVERT: G 518 MET cc_start: 0.8116 (tpp) cc_final: 0.7885 (tpp) REVERT: G 568 MET cc_start: 0.8583 (mmm) cc_final: 0.8012 (mmm) REVERT: H 627 MET cc_start: 0.9445 (ttt) cc_final: 0.9032 (tmm) REVERT: H 639 ARG cc_start: 0.9054 (mmm-85) cc_final: 0.8840 (mmm-85) REVERT: H 650 PHE cc_start: 0.8641 (t80) cc_final: 0.8392 (t80) REVERT: H 686 ASN cc_start: 0.9191 (p0) cc_final: 0.8968 (p0) outliers start: 31 outliers final: 12 residues processed: 97 average time/residue: 0.2630 time to fit residues: 37.3325 Evaluate side-chains 83 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain H residue 620 ASP Chi-restraints excluded: chain H residue 700 LEU Chi-restraints excluded: chain H residue 708 ASP Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 100 optimal weight: 0.0970 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13337 Z= 0.269 Angle : 0.573 7.322 18753 Z= 0.321 Chirality : 0.037 0.192 2110 Planarity : 0.003 0.046 1783 Dihedral : 26.277 179.273 3100 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.60 % Allowed : 12.21 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.26), residues: 1140 helix: 2.26 (0.21), residues: 633 sheet: 0.31 (0.62), residues: 52 loop : -0.25 (0.33), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 443 HIS 0.002 0.001 HIS G 391 PHE 0.016 0.001 PHE H 668 TYR 0.019 0.001 TYR B 652 ARG 0.007 0.000 ARG H 719 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 67 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: A 517 MET cc_start: 0.7910 (tpp) cc_final: 0.7598 (tpp) REVERT: A 563 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7566 (ptp90) REVERT: A 567 MET cc_start: 0.8931 (mmt) cc_final: 0.8699 (tpt) REVERT: B 627 MET cc_start: 0.9572 (ttt) cc_final: 0.9119 (tmm) REVERT: B 647 ASN cc_start: 0.8893 (t0) cc_final: 0.8655 (t0) REVERT: B 693 ASN cc_start: 0.9601 (m-40) cc_final: 0.9264 (p0) REVERT: G 440 MET cc_start: 0.9385 (tpp) cc_final: 0.8964 (tpp) REVERT: G 518 MET cc_start: 0.8157 (tpp) cc_final: 0.7939 (tpp) REVERT: G 568 MET cc_start: 0.8602 (mmm) cc_final: 0.8048 (mmm) REVERT: H 627 MET cc_start: 0.9470 (ttt) cc_final: 0.9106 (tmm) REVERT: H 639 ARG cc_start: 0.9087 (mmm-85) cc_final: 0.8828 (mmm-85) REVERT: H 650 PHE cc_start: 0.8622 (t80) cc_final: 0.8375 (t80) REVERT: H 693 ASN cc_start: 0.9609 (m-40) cc_final: 0.9306 (p0) outliers start: 26 outliers final: 17 residues processed: 88 average time/residue: 0.2578 time to fit residues: 33.4123 Evaluate side-chains 84 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain H residue 620 ASP Chi-restraints excluded: chain H residue 708 ASP Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 0.0020 chunk 103 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 61 optimal weight: 4.9990 chunk 108 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13337 Z= 0.156 Angle : 0.512 8.395 18753 Z= 0.289 Chirality : 0.035 0.154 2110 Planarity : 0.003 0.044 1783 Dihedral : 26.176 177.846 3100 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.60 % Allowed : 14.61 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.27), residues: 1140 helix: 2.34 (0.21), residues: 644 sheet: 0.93 (0.58), residues: 64 loop : -0.20 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 442 HIS 0.002 0.000 HIS G 343 PHE 0.012 0.001 PHE H 668 TYR 0.021 0.001 TYR B 652 ARG 0.004 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 1.437 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.9440 (tpp) cc_final: 0.9091 (mmt) REVERT: A 517 MET cc_start: 0.8023 (tpp) cc_final: 0.7679 (tpp) REVERT: A 563 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7247 (ptp90) REVERT: A 567 MET cc_start: 0.8882 (mmt) cc_final: 0.8536 (tpt) REVERT: B 627 MET cc_start: 0.9561 (ttt) cc_final: 0.9096 (tmm) REVERT: B 647 ASN cc_start: 0.8924 (t0) cc_final: 0.8707 (t0) REVERT: B 693 ASN cc_start: 0.9557 (m-40) cc_final: 0.9196 (p0) REVERT: G 440 MET cc_start: 0.9345 (tpp) cc_final: 0.8955 (tpp) REVERT: G 518 MET cc_start: 0.8185 (tpp) cc_final: 0.7956 (tpp) REVERT: G 568 MET cc_start: 0.8724 (mmm) cc_final: 0.8188 (mmm) REVERT: H 627 MET cc_start: 0.9451 (ttt) cc_final: 0.9054 (tmm) REVERT: H 639 ARG cc_start: 0.9070 (mmm-85) cc_final: 0.8795 (mmm-85) REVERT: H 650 PHE cc_start: 0.8693 (t80) cc_final: 0.8427 (t80) outliers start: 16 outliers final: 7 residues processed: 86 average time/residue: 0.2847 time to fit residues: 36.2290 Evaluate side-chains 74 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 708 ASP Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN A 440 ASN ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13337 Z= 0.203 Angle : 0.537 6.691 18753 Z= 0.300 Chirality : 0.035 0.166 2110 Planarity : 0.003 0.042 1783 Dihedral : 26.210 179.039 3100 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.40 % Allowed : 14.31 % Favored : 83.28 % 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: 2.21 (0.27), residues: 1140 helix: 2.57 (0.21), residues: 637 sheet: 1.19 (0.64), residues: 52 loop : -0.11 (0.33), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 323 HIS 0.002 0.000 HIS G 391 PHE 0.013 0.001 PHE H 668 TYR 0.012 0.001 TYR B 652 ARG 0.011 0.000 ARG B 703 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 184 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7791 (t80) REVERT: A 480 MET cc_start: 0.9428 (mmm) cc_final: 0.9142 (mmp) REVERT: A 563 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7313 (ptp90) REVERT: B 627 MET cc_start: 0.9563 (ttt) cc_final: 0.9081 (tmm) REVERT: B 647 ASN cc_start: 0.8954 (t0) cc_final: 0.8749 (t0) REVERT: B 693 ASN cc_start: 0.9565 (m-40) cc_final: 0.9179 (t0) REVERT: G 440 MET cc_start: 0.9358 (tpp) cc_final: 0.8994 (tpp) REVERT: G 518 MET cc_start: 0.8223 (tpp) cc_final: 0.7996 (tpp) REVERT: G 568 MET cc_start: 0.8711 (mmm) cc_final: 0.8068 (mmm) REVERT: H 627 MET cc_start: 0.9443 (ttt) cc_final: 0.9070 (tmm) REVERT: H 639 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8790 (mmm-85) REVERT: H 650 PHE cc_start: 0.8675 (t80) cc_final: 0.8397 (t80) outliers start: 24 outliers final: 17 residues processed: 83 average time/residue: 0.2618 time to fit residues: 32.3326 Evaluate side-chains 84 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain H residue 620 ASP Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 708 ASP Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13337 Z= 0.196 Angle : 0.534 9.458 18753 Z= 0.298 Chirality : 0.035 0.153 2110 Planarity : 0.003 0.041 1783 Dihedral : 26.217 179.246 3100 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.20 % Allowed : 14.71 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.27), residues: 1140 helix: 2.53 (0.21), residues: 642 sheet: 0.59 (0.60), residues: 67 loop : -0.09 (0.34), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 442 HIS 0.001 0.000 HIS A 546 PHE 0.010 0.001 PHE H 668 TYR 0.011 0.001 TYR G 511 ARG 0.008 0.000 ARG B 703 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 184 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7840 (t80) REVERT: A 480 MET cc_start: 0.9423 (mmm) cc_final: 0.9149 (mmp) REVERT: A 517 MET cc_start: 0.8054 (tpp) cc_final: 0.7734 (tpp) REVERT: A 563 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7522 (ptp90) REVERT: A 567 MET cc_start: 0.8935 (tpt) cc_final: 0.8682 (tpt) REVERT: B 627 MET cc_start: 0.9554 (ttt) cc_final: 0.9071 (tmm) REVERT: B 693 ASN cc_start: 0.9551 (m-40) cc_final: 0.9067 (t0) REVERT: G 440 MET cc_start: 0.9348 (tpp) cc_final: 0.8496 (tpp) REVERT: G 518 MET cc_start: 0.8226 (tpp) cc_final: 0.8024 (tpp) REVERT: G 538 MET cc_start: 0.8968 (tpp) cc_final: 0.8694 (tpp) REVERT: H 627 MET cc_start: 0.9459 (ttt) cc_final: 0.9053 (tmm) REVERT: H 639 ARG cc_start: 0.9057 (mmm-85) cc_final: 0.8807 (mmm-85) REVERT: H 650 PHE cc_start: 0.8679 (t80) cc_final: 0.8405 (t80) outliers start: 22 outliers final: 16 residues processed: 84 average time/residue: 0.2590 time to fit residues: 32.5545 Evaluate side-chains 84 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 708 ASP Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.0000 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 0.0770 chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13337 Z= 0.144 Angle : 0.520 10.860 18753 Z= 0.289 Chirality : 0.035 0.150 2110 Planarity : 0.003 0.049 1783 Dihedral : 26.092 177.433 3100 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.80 % Allowed : 15.12 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.27), residues: 1140 helix: 2.49 (0.21), residues: 652 sheet: 0.81 (0.59), residues: 67 loop : -0.18 (0.34), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 442 HIS 0.002 0.000 HIS G 343 PHE 0.011 0.001 PHE H 668 TYR 0.009 0.001 TYR G 511 ARG 0.014 0.000 ARG B 703 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: A 184 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7792 (t80) REVERT: A 476 MET cc_start: 0.9453 (tpp) cc_final: 0.9174 (mmt) REVERT: A 517 MET cc_start: 0.8011 (tpp) cc_final: 0.7675 (tpp) REVERT: B 627 MET cc_start: 0.9533 (OUTLIER) cc_final: 0.9038 (tmm) REVERT: B 693 ASN cc_start: 0.9482 (m-40) cc_final: 0.9020 (t0) REVERT: B 732 GLU cc_start: 0.8388 (pt0) cc_final: 0.7508 (tm-30) REVERT: G 538 MET cc_start: 0.8902 (tpp) cc_final: 0.8561 (tpp) REVERT: G 568 MET cc_start: 0.8734 (mmm) cc_final: 0.8178 (mmm) REVERT: H 627 MET cc_start: 0.9453 (ttt) cc_final: 0.9023 (tmm) REVERT: H 639 ARG cc_start: 0.9009 (mmm-85) cc_final: 0.8794 (mmm-85) REVERT: H 650 PHE cc_start: 0.8766 (t80) cc_final: 0.8438 (t80) outliers start: 18 outliers final: 12 residues processed: 84 average time/residue: 0.2646 time to fit residues: 33.0601 Evaluate side-chains 81 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 6.9990 chunk 115 optimal weight: 0.2980 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 GLN G 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13337 Z= 0.148 Angle : 0.530 12.282 18753 Z= 0.290 Chirality : 0.034 0.156 2110 Planarity : 0.003 0.037 1783 Dihedral : 26.072 176.551 3100 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.50 % Allowed : 15.52 % Favored : 82.98 % 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: 2.23 (0.26), residues: 1140 helix: 2.52 (0.21), residues: 651 sheet: 1.44 (0.63), residues: 54 loop : -0.13 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 442 HIS 0.002 0.000 HIS G 343 PHE 0.016 0.001 PHE H 668 TYR 0.011 0.001 TYR G 511 ARG 0.008 0.000 ARG B 703 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.9466 (tpp) cc_final: 0.9141 (mmt) REVERT: A 517 MET cc_start: 0.8023 (tpp) cc_final: 0.7685 (tpp) REVERT: B 627 MET cc_start: 0.9556 (ttt) cc_final: 0.9050 (tmm) REVERT: B 693 ASN cc_start: 0.9487 (m-40) cc_final: 0.9039 (t0) REVERT: B 732 GLU cc_start: 0.8372 (pt0) cc_final: 0.7441 (tm-30) REVERT: G 213 LEU cc_start: 0.9218 (mp) cc_final: 0.8571 (tp) REVERT: G 440 MET cc_start: 0.9279 (tpp) cc_final: 0.8940 (tpp) REVERT: G 538 MET cc_start: 0.8862 (tpp) cc_final: 0.8522 (tpp) REVERT: G 568 MET cc_start: 0.8691 (mmm) cc_final: 0.8100 (mmm) REVERT: H 627 MET cc_start: 0.9445 (ttt) cc_final: 0.9004 (tmm) REVERT: H 650 PHE cc_start: 0.8759 (t80) cc_final: 0.8438 (t80) REVERT: H 686 ASN cc_start: 0.9231 (p0) cc_final: 0.9017 (p0) outliers start: 15 outliers final: 14 residues processed: 81 average time/residue: 0.2487 time to fit residues: 30.4964 Evaluate side-chains 82 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN G 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13337 Z= 0.203 Angle : 0.553 12.456 18753 Z= 0.302 Chirality : 0.035 0.147 2110 Planarity : 0.003 0.043 1783 Dihedral : 26.164 178.107 3100 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.60 % Allowed : 15.12 % Favored : 83.28 % 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: 2.37 (0.27), residues: 1140 helix: 2.64 (0.21), residues: 647 sheet: 1.50 (0.60), residues: 50 loop : -0.04 (0.33), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 323 HIS 0.002 0.000 HIS G 391 PHE 0.016 0.001 PHE H 668 TYR 0.011 0.001 TYR G 511 ARG 0.014 0.000 ARG B 703 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 184 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 476 MET cc_start: 0.9412 (tpp) cc_final: 0.9195 (mmt) REVERT: A 517 MET cc_start: 0.8034 (tpp) cc_final: 0.7697 (tpp) REVERT: B 627 MET cc_start: 0.9580 (OUTLIER) cc_final: 0.9049 (tmm) REVERT: B 693 ASN cc_start: 0.9523 (m-40) cc_final: 0.9081 (t0) REVERT: G 213 LEU cc_start: 0.9245 (mp) cc_final: 0.8721 (mp) REVERT: G 538 MET cc_start: 0.8995 (tpp) cc_final: 0.8709 (tpp) REVERT: G 568 MET cc_start: 0.8712 (mmm) cc_final: 0.8095 (mmm) REVERT: H 627 MET cc_start: 0.9454 (ttt) cc_final: 0.9019 (tmm) REVERT: H 650 PHE cc_start: 0.8703 (t80) cc_final: 0.8406 (t80) outliers start: 16 outliers final: 14 residues processed: 80 average time/residue: 0.2510 time to fit residues: 30.3084 Evaluate side-chains 83 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.047860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.034838 restraints weight = 82295.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.036063 restraints weight = 37206.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.036878 restraints weight = 22860.743| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13337 Z= 0.191 Angle : 0.551 12.661 18753 Z= 0.302 Chirality : 0.035 0.152 2110 Planarity : 0.003 0.037 1783 Dihedral : 26.181 178.437 3100 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.90 % Allowed : 15.02 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.27), residues: 1140 helix: 2.69 (0.21), residues: 641 sheet: 1.39 (0.58), residues: 67 loop : -0.01 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 442 HIS 0.002 0.000 HIS G 343 PHE 0.016 0.001 PHE H 668 TYR 0.011 0.001 TYR G 511 ARG 0.008 0.000 ARG B 703 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.32 seconds wall clock time: 40 minutes 52.91 seconds (2452.91 seconds total)