Starting phenix.real_space_refine on Thu Feb 15 10:21:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5a_20254/02_2024/6p5a_20254_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5a_20254/02_2024/6p5a_20254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5a_20254/02_2024/6p5a_20254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5a_20254/02_2024/6p5a_20254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5a_20254/02_2024/6p5a_20254_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5a_20254/02_2024/6p5a_20254_updated.pdb" } resolution = 3.6 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= 0.004 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 142 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 7150 2.51 5 N 2076 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 273": "OD1" <-> "OD2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "G ASP 273": "OD1" <-> "OD2" Residue "G ASP 279": "OD1" <-> "OD2" Residue "G PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 339": "OD1" <-> "OD2" Residue "G GLU 388": "OE1" <-> "OE2" Residue "G GLU 431": "OE1" <-> "OE2" Residue "H GLU 670": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11948 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3568 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 428} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 896 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "G" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3568 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 428} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Chain: "K" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 896 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "A" 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} 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: 6.86, per 1000 atoms: 0.57 Number of scatterers: 11948 At special positions: 0 Unit cell: (126.44, 110.2, 106.72, 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 142 15.00 Mg 4 11.99 O 2540 8.00 N 2076 7.00 C 7150 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: 5.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 6 sheets defined 50.5% alpha, 8.0% beta 54 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.673A 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: 3.790A pdb=" N HIS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 198 removed outlier: 3.652A 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 removed outlier: 3.567A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) 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 447 Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.376A 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 129 through 139 removed outlier: 3.673A pdb=" N GLU G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 148 Processing helix chain 'G' and resid 159 through 169 Processing helix chain 'G' and resid 173 through 182 removed outlier: 3.791A pdb=" N HIS G 178 " --> pdb=" O ARG G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 198 removed outlier: 3.651A pdb=" N ASP G 198 " --> pdb=" O ARG G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 212 Processing helix chain 'G' and resid 280 through 293 Processing helix chain 'G' and resid 306 through 314 removed outlier: 3.568A pdb=" N LEU G 311 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 353 Processing helix chain 'G' and resid 366 through 375 Processing helix chain 'G' and resid 388 through 391 No H-bonds generated for 'chain 'G' and resid 388 through 391' Processing helix chain 'G' and resid 401 through 407 Processing helix chain 'G' and resid 410 through 421 Processing helix chain 'G' and resid 429 through 447 Processing helix chain 'G' and resid 466 through 479 removed outlier: 4.377A pdb=" N ASP G 471 " --> pdb=" O ASP G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 514 Processing helix chain 'G' and resid 522 through 525 Processing helix chain 'G' and resid 528 through 539 Processing helix chain 'G' and resid 549 through 562 Processing helix chain 'G' and resid 565 through 567 No H-bonds generated for 'chain 'G' and resid 565 through 567' 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: 9.508A pdb=" N LYS A 333 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL A 298 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU A 227 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE A 300 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE A 229 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER A 302 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N GLU A 231 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A 259 " --> pdb=" O PRO A 269 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY A 261 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 7.122A 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: 3.796A 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 323 through 325 removed outlier: 9.508A pdb=" N LYS G 333 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL G 298 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU G 227 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE G 300 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE G 229 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER G 302 " --> pdb=" O PHE G 229 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N GLU G 231 " --> pdb=" O SER G 302 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL G 259 " --> pdb=" O PRO G 269 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY G 261 " --> pdb=" O LYS G 267 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS G 267 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 239 through 241 removed outlier: 3.795A pdb=" N ILE G 246 " --> pdb=" O ASP G 241 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 356 through 358 414 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 256 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 5.69 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: 2863 1.34 - 1.45: 3084 1.45 - 1.57: 6177 1.57 - 1.69: 274 1.69 - 1.81: 56 Bond restraints: 12454 Sorted by residual: bond pdb=" C THR A 548 " pdb=" N PRO A 549 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.90e+00 bond pdb=" C THR G 548 " pdb=" N PRO G 549 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.85e+00 bond pdb=" C3' DT E -2 " pdb=" C2' DT E -2 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.08e+00 bond pdb=" C3' DT K -2 " pdb=" C2' DT K -2 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.05e+00 bond pdb=" O5' DA E -3 " pdb=" C5' DA E -3 " ideal model delta sigma weight residual 1.423 1.394 0.029 3.00e-02 1.11e+03 9.50e-01 ... (remaining 12449 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.50: 985 106.50 - 113.38: 6744 113.38 - 120.25: 4782 120.25 - 127.13: 4543 127.13 - 134.01: 344 Bond angle restraints: 17398 Sorted by residual: angle pdb=" C4' DA K -3 " pdb=" C3' DA K -3 " pdb=" C2' DA K -3 " ideal model delta sigma weight residual 102.40 107.10 -4.70 1.50e+00 4.44e-01 9.83e+00 angle pdb=" C4' DA E -3 " pdb=" C3' DA E -3 " pdb=" C2' DA E -3 " ideal model delta sigma weight residual 102.40 107.10 -4.70 1.50e+00 4.44e-01 9.80e+00 angle pdb=" C3' DA K -3 " pdb=" O3' DA K -3 " pdb=" P DT K -2 " ideal model delta sigma weight residual 120.20 116.46 3.74 1.50e+00 4.44e-01 6.21e+00 angle pdb=" C3' DA E -3 " pdb=" O3' DA E -3 " pdb=" P DT E -2 " ideal model delta sigma weight residual 120.20 116.46 3.74 1.50e+00 4.44e-01 6.21e+00 angle pdb=" C4 DT E -13 " pdb=" C5 DT E -13 " pdb=" C7 DT E -13 " ideal model delta sigma weight residual 122.40 118.97 3.43 1.50e+00 4.44e-01 5.23e+00 ... (remaining 17393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.76: 6564 34.76 - 69.51: 518 69.51 - 104.27: 12 104.27 - 139.02: 4 139.02 - 173.78: 6 Dihedral angle restraints: 7104 sinusoidal: 3798 harmonic: 3306 Sorted by residual: 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 -31.60 136.20 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C8 GTP G 602 " pdb=" C1' GTP G 602 " pdb=" N9 GTP G 602 " pdb=" O4' GTP G 602 " ideal model delta sinusoidal sigma weight residual 104.59 -31.56 136.16 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C4' DT E -13 " pdb=" C3' DT E -13 " pdb=" O3' DT E -13 " pdb=" P DT E -12 " ideal model delta sinusoidal sigma weight residual -140.00 33.78 -173.78 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1645 0.048 - 0.095: 241 0.095 - 0.143: 55 0.143 - 0.191: 3 0.191 - 0.239: 2 Chirality restraints: 1946 Sorted by residual: chirality pdb=" C3' DA K -3 " pdb=" C4' DA K -3 " pdb=" O3' DA K -3 " pdb=" C2' DA K -3 " both_signs ideal model delta sigma weight residual False -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' DA E -3 " pdb=" C4' DA E -3 " pdb=" O3' DA E -3 " pdb=" C2' DA E -3 " both_signs ideal model delta sigma weight residual False -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO G 549 " pdb=" N PRO G 549 " pdb=" C PRO G 549 " pdb=" CB PRO G 549 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 1943 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN G 268 " -0.034 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO G 269 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 269 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 269 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 268 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 269 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 172 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO G 173 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " 0.023 5.00e-02 4.00e+02 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 30 2.49 - 3.09: 7813 3.09 - 3.70: 18376 3.70 - 4.30: 27938 4.30 - 4.90: 43492 Nonbonded interactions: 97649 Sorted by model distance: nonbonded pdb=" OD1 ASN A 440 " pdb="MG MG A 602 " model vdw 1.890 2.170 nonbonded pdb=" OD1 ASN G 440 " pdb="MG MG G 603 " model vdw 1.907 2.170 nonbonded pdb=" O3' DA I 9 " pdb="MG MG G 601 " model vdw 2.077 2.170 nonbonded pdb=" O3' DA C 9 " pdb="MG MG A 603 " model vdw 2.078 2.170 nonbonded pdb=" OD2 ASP A 303 " pdb="MG MG A 603 " model vdw 2.135 2.170 ... (remaining 97644 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 128 through 569 or resid 603)) selection = (chain 'G' and (resid 128 through 569 or resid 603)) } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' 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: 0.720 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: 4.070 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 38.040 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 0.032 12454 Z= 0.145 Angle : 0.526 5.475 17398 Z= 0.316 Chirality : 0.037 0.239 1946 Planarity : 0.004 0.052 1730 Dihedral : 20.140 173.780 4960 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -1.69 (0.22), residues: 1112 helix: -0.46 (0.18), residues: 622 sheet: -2.11 (0.47), residues: 60 loop : -1.85 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 442 HIS 0.002 0.001 HIS G 546 PHE 0.014 0.001 PHE A 272 TYR 0.008 0.001 TYR H 629 ARG 0.002 0.000 ARG G 569 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.257 Fit side-chains REVERT: A 273 ASP cc_start: 0.7712 (t70) cc_final: 0.7429 (t0) REVERT: A 476 MET cc_start: 0.8352 (tpp) cc_final: 0.7614 (tpt) REVERT: A 563 ARG cc_start: 0.7328 (ptm-80) cc_final: 0.6931 (ptm160) REVERT: A 567 MET cc_start: 0.7410 (tpp) cc_final: 0.7168 (tpt) REVERT: B 700 LEU cc_start: 0.8528 (tt) cc_final: 0.7511 (mt) REVERT: G 239 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7741 (mm-30) REVERT: G 273 ASP cc_start: 0.7731 (t70) cc_final: 0.7445 (t0) REVERT: G 476 MET cc_start: 0.8359 (tpp) cc_final: 0.7617 (tpt) REVERT: G 563 ARG cc_start: 0.7332 (ptm-80) cc_final: 0.6935 (ptm160) REVERT: G 567 MET cc_start: 0.7427 (tpp) cc_final: 0.7150 (tpt) REVERT: H 700 LEU cc_start: 0.8525 (tt) cc_final: 0.7504 (mt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2933 time to fit residues: 91.4925 Evaluate side-chains 134 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 546 HIS B 685 ASN B 686 ASN G 150 ASN G 546 HIS H 685 ASN H 686 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 12454 Z= 0.484 Angle : 0.681 7.672 17398 Z= 0.373 Chirality : 0.045 0.175 1946 Planarity : 0.005 0.060 1730 Dihedral : 25.603 174.642 2698 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.78 % Allowed : 9.52 % Favored : 87.70 % 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: -0.61 (0.24), residues: 1112 helix: 0.33 (0.20), residues: 592 sheet: -1.31 (0.50), residues: 66 loop : -1.16 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 312 HIS 0.005 0.001 HIS A 326 PHE 0.017 0.002 PHE G 324 TYR 0.019 0.002 TYR A 559 ARG 0.005 0.001 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 1.182 Fit side-chains REVERT: A 476 MET cc_start: 0.8751 (tpp) cc_final: 0.8131 (tpt) REVERT: A 567 MET cc_start: 0.7550 (tpp) cc_final: 0.7332 (tpt) REVERT: G 476 MET cc_start: 0.8748 (tpp) cc_final: 0.8118 (tpt) REVERT: G 567 MET cc_start: 0.7561 (tpp) cc_final: 0.7342 (tpt) outliers start: 28 outliers final: 19 residues processed: 142 average time/residue: 0.2380 time to fit residues: 49.1957 Evaluate side-chains 120 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 565 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS B 669 GLN ** G 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 HIS H 669 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12454 Z= 0.217 Angle : 0.509 5.925 17398 Z= 0.285 Chirality : 0.037 0.132 1946 Planarity : 0.004 0.062 1730 Dihedral : 24.845 176.265 2698 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.59 % Allowed : 13.19 % Favored : 85.22 % 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: 0.19 (0.25), residues: 1112 helix: 0.97 (0.21), residues: 600 sheet: -0.17 (0.59), residues: 60 loop : -0.94 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 312 HIS 0.002 0.001 HIS A 342 PHE 0.010 0.001 PHE G 493 TYR 0.017 0.001 TYR G 559 ARG 0.004 0.000 ARG G 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 1.190 Fit side-chains REVERT: A 395 SER cc_start: 0.8191 (m) cc_final: 0.7872 (t) REVERT: A 476 MET cc_start: 0.8612 (tpp) cc_final: 0.8099 (tpt) REVERT: B 681 HIS cc_start: 0.7498 (t-90) cc_final: 0.7225 (t70) REVERT: G 395 SER cc_start: 0.8166 (m) cc_final: 0.7852 (t) REVERT: G 476 MET cc_start: 0.8613 (tpp) cc_final: 0.8085 (tpt) REVERT: H 681 HIS cc_start: 0.7498 (t-90) cc_final: 0.7228 (t70) outliers start: 16 outliers final: 2 residues processed: 119 average time/residue: 0.2087 time to fit residues: 38.2959 Evaluate side-chains 97 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain G residue 415 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12454 Z= 0.360 Angle : 0.585 6.904 17398 Z= 0.320 Chirality : 0.040 0.140 1946 Planarity : 0.004 0.062 1730 Dihedral : 25.153 173.468 2698 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.98 % Allowed : 15.18 % Favored : 82.84 % 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: 0.25 (0.25), residues: 1112 helix: 0.93 (0.21), residues: 602 sheet: -0.45 (0.57), residues: 66 loop : -0.70 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 312 HIS 0.004 0.001 HIS A 326 PHE 0.014 0.002 PHE G 324 TYR 0.019 0.002 TYR G 559 ARG 0.006 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.210 Fit side-chains REVERT: A 476 MET cc_start: 0.8678 (tpp) cc_final: 0.8094 (tpt) REVERT: G 476 MET cc_start: 0.8679 (tpp) cc_final: 0.8080 (tpt) outliers start: 20 outliers final: 18 residues processed: 121 average time/residue: 0.2001 time to fit residues: 38.1338 Evaluate side-chains 120 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 450 LEU Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain H residue 665 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7869 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12454 Z= 0.208 Angle : 0.508 5.932 17398 Z= 0.281 Chirality : 0.036 0.133 1946 Planarity : 0.004 0.061 1730 Dihedral : 24.713 176.197 2698 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.19 % Allowed : 16.57 % Favored : 82.24 % 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: 0.56 (0.25), residues: 1112 helix: 1.21 (0.21), residues: 610 sheet: 0.16 (0.60), residues: 60 loop : -0.74 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 312 HIS 0.002 0.000 HIS G 326 PHE 0.010 0.001 PHE G 493 TYR 0.018 0.001 TYR G 559 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.219 Fit side-chains REVERT: A 476 MET cc_start: 0.8590 (tpp) cc_final: 0.8114 (tpt) REVERT: B 681 HIS cc_start: 0.7497 (t-90) cc_final: 0.7224 (t70) REVERT: G 476 MET cc_start: 0.8589 (tpp) cc_final: 0.8102 (tpt) REVERT: H 681 HIS cc_start: 0.7501 (t-90) cc_final: 0.7229 (t70) outliers start: 12 outliers final: 8 residues processed: 113 average time/residue: 0.2284 time to fit residues: 38.6104 Evaluate side-chains 105 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 450 LEU Chi-restraints excluded: chain G residue 452 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7845 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12454 Z= 0.179 Angle : 0.500 6.402 17398 Z= 0.276 Chirality : 0.036 0.131 1946 Planarity : 0.004 0.058 1730 Dihedral : 24.555 175.679 2698 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.39 % Allowed : 16.27 % Favored : 82.34 % 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 (0.26), residues: 1112 helix: 1.42 (0.21), residues: 616 sheet: 0.53 (0.61), residues: 60 loop : -0.60 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 312 HIS 0.002 0.000 HIS G 326 PHE 0.009 0.001 PHE G 493 TYR 0.019 0.001 TYR G 559 ARG 0.006 0.000 ARG G 540 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.195 Fit side-chains REVERT: A 395 SER cc_start: 0.8244 (m) cc_final: 0.7846 (t) REVERT: A 476 MET cc_start: 0.8643 (tpp) cc_final: 0.8030 (tpt) REVERT: B 681 HIS cc_start: 0.7443 (t-90) cc_final: 0.7176 (t70) REVERT: G 395 SER cc_start: 0.8272 (m) cc_final: 0.7892 (t) REVERT: G 476 MET cc_start: 0.8660 (tpp) cc_final: 0.8035 (tpt) REVERT: H 681 HIS cc_start: 0.7445 (t-90) cc_final: 0.7178 (t70) outliers start: 14 outliers final: 10 residues processed: 121 average time/residue: 0.1942 time to fit residues: 36.9683 Evaluate side-chains 118 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 415 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN G 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12454 Z= 0.207 Angle : 0.519 6.492 17398 Z= 0.284 Chirality : 0.036 0.128 1946 Planarity : 0.004 0.058 1730 Dihedral : 24.610 175.472 2698 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.59 % Allowed : 17.36 % Favored : 81.05 % 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: 0.94 (0.26), residues: 1112 helix: 1.49 (0.21), residues: 612 sheet: 0.36 (0.60), residues: 66 loop : -0.55 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 312 HIS 0.002 0.000 HIS G 326 PHE 0.010 0.001 PHE G 493 TYR 0.026 0.001 TYR G 559 ARG 0.006 0.000 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.336 Fit side-chains REVERT: A 395 SER cc_start: 0.8228 (m) cc_final: 0.7806 (t) REVERT: A 476 MET cc_start: 0.8672 (tpp) cc_final: 0.8052 (tpt) REVERT: B 681 HIS cc_start: 0.7469 (t-90) cc_final: 0.7250 (t70) REVERT: G 476 MET cc_start: 0.8706 (tpp) cc_final: 0.8068 (tpt) REVERT: H 681 HIS cc_start: 0.7464 (t-90) cc_final: 0.7245 (t70) outliers start: 16 outliers final: 12 residues processed: 128 average time/residue: 0.2066 time to fit residues: 40.5114 Evaluate side-chains 124 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain H residue 665 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 0.0070 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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: 0.7840 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12454 Z= 0.186 Angle : 0.512 6.920 17398 Z= 0.279 Chirality : 0.036 0.129 1946 Planarity : 0.003 0.057 1730 Dihedral : 24.516 176.109 2698 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.19 % Allowed : 17.36 % Favored : 81.45 % 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: 1.10 (0.26), residues: 1112 helix: 1.62 (0.21), residues: 612 sheet: 0.80 (0.61), residues: 60 loop : -0.52 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 312 HIS 0.002 0.000 HIS G 326 PHE 0.009 0.001 PHE G 493 TYR 0.024 0.001 TYR G 559 ARG 0.005 0.000 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.197 Fit side-chains REVERT: A 395 SER cc_start: 0.8232 (m) cc_final: 0.7822 (t) REVERT: A 476 MET cc_start: 0.8667 (tpp) cc_final: 0.8065 (tpt) REVERT: G 395 SER cc_start: 0.8303 (m) cc_final: 0.7912 (t) REVERT: G 476 MET cc_start: 0.8683 (tpp) cc_final: 0.8094 (tpt) outliers start: 12 outliers final: 12 residues processed: 123 average time/residue: 0.2106 time to fit residues: 39.3903 Evaluate side-chains 122 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 665 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.0570 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.0170 chunk 84 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12454 Z= 0.163 Angle : 0.506 7.379 17398 Z= 0.275 Chirality : 0.035 0.128 1946 Planarity : 0.003 0.055 1730 Dihedral : 24.451 176.321 2698 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.09 % Allowed : 17.96 % Favored : 80.95 % 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: 1.17 (0.26), residues: 1112 helix: 1.69 (0.21), residues: 614 sheet: 0.91 (0.61), residues: 60 loop : -0.54 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 323 HIS 0.002 0.000 HIS A 326 PHE 0.009 0.001 PHE G 493 TYR 0.024 0.001 TYR G 559 ARG 0.005 0.000 ARG G 540 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.150 Fit side-chains REVERT: A 395 SER cc_start: 0.8228 (m) cc_final: 0.7808 (t) REVERT: A 476 MET cc_start: 0.8634 (tpp) cc_final: 0.8046 (tpt) REVERT: G 395 SER cc_start: 0.8262 (m) cc_final: 0.7866 (t) REVERT: G 476 MET cc_start: 0.8664 (tpp) cc_final: 0.8091 (tpt) outliers start: 11 outliers final: 11 residues processed: 124 average time/residue: 0.2245 time to fit residues: 41.7970 Evaluate side-chains 122 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 665 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.0770 chunk 119 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 685 ASN H 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12454 Z= 0.160 Angle : 0.505 7.560 17398 Z= 0.274 Chirality : 0.035 0.127 1946 Planarity : 0.003 0.053 1730 Dihedral : 24.442 176.429 2698 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.99 % Allowed : 18.15 % Favored : 80.85 % 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: 1.27 (0.26), residues: 1112 helix: 1.77 (0.21), residues: 614 sheet: 0.71 (0.59), residues: 70 loop : -0.47 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 323 HIS 0.002 0.000 HIS G 326 PHE 0.009 0.001 PHE G 493 TYR 0.025 0.001 TYR G 559 ARG 0.005 0.000 ARG G 540 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.151 Fit side-chains REVERT: A 476 MET cc_start: 0.8647 (tpp) cc_final: 0.8048 (tpt) REVERT: G 395 SER cc_start: 0.8302 (m) cc_final: 0.7912 (t) REVERT: G 476 MET cc_start: 0.8650 (tpp) cc_final: 0.8076 (tpt) outliers start: 10 outliers final: 10 residues processed: 121 average time/residue: 0.2123 time to fit residues: 39.1859 Evaluate side-chains 121 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 665 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 685 ASN H 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116353 restraints weight = 14955.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120106 restraints weight = 9026.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122748 restraints weight = 6441.270| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12454 Z= 0.170 Angle : 0.506 7.590 17398 Z= 0.274 Chirality : 0.035 0.127 1946 Planarity : 0.003 0.054 1730 Dihedral : 24.452 176.370 2698 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.99 % Allowed : 18.15 % Favored : 80.85 % 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: 1.27 (0.26), residues: 1112 helix: 1.75 (0.21), residues: 612 sheet: 0.73 (0.59), residues: 70 loop : -0.43 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 312 HIS 0.002 0.000 HIS G 326 PHE 0.009 0.001 PHE G 493 TYR 0.025 0.001 TYR G 559 ARG 0.005 0.000 ARG G 540 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2102.65 seconds wall clock time: 39 minutes 24.19 seconds (2364.19 seconds total)