Starting phenix.real_space_refine on Fri Aug 22 16:12:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gp5_34190/08_2025/8gp5_34190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gp5_34190/08_2025/8gp5_34190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gp5_34190/08_2025/8gp5_34190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gp5_34190/08_2025/8gp5_34190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gp5_34190/08_2025/8gp5_34190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gp5_34190/08_2025/8gp5_34190.map" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 3437 2.51 5 N 901 2.21 5 O 1099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5470 Number of models: 1 Model: "" Number of chains: 11 Chain: "E" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "X" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3265 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 19, 'TRANS': 390} Chain breaks: 8 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.39, per 1000 atoms: 0.25 Number of scatterers: 5470 At special positions: 0 Unit cell: (77.38, 78.44, 120.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1099 8.00 N 901 7.00 C 3437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS X 54 " - pdb=" SG CYS X 74 " distance=2.03 Simple disulfide: pdb=" SG CYS X 218 " - pdb=" SG CYS X 247 " distance=2.04 Simple disulfide: pdb=" SG CYS X 228 " - pdb=" SG CYS X 239 " distance=2.03 Simple disulfide: pdb=" SG CYS X 296 " - pdb=" SG CYS X 331 " distance=2.03 Simple disulfide: pdb=" SG CYS X 378 " - pdb=" SG CYS X 445 " distance=2.03 Simple disulfide: pdb=" SG CYS X 385 " - pdb=" SG CYS X 418 " distance=2.03 Simple disulfide: pdb=" SG CYS X 501 " - pdb=" SG CYS X 605 " distance=2.03 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 1 " - " ASN X 234 " " NAG B 1 " - " ASN X 262 " " NAG C 1 " - " ASN X 276 " " NAG D 1 " - " ASN X 334 " " NAG G 1 " - " ASN X 386 " " NAG H 1 " - " ASN X 625 " " NAG N 1 " - " ASN X 88 " " NAG X 701 " - " ASN X 241 " " NAG X 702 " - " ASN X 289 " " NAG X 703 " - " ASN X 448 " " NAG X 704 " - " ASN X 339 " " NAG X 705 " - " ASN X 444 " " NAG X 706 " - " ASN X 611 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 192.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1198 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 16.7% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 99 through 114 removed outlier: 3.773A pdb=" N GLN X 103 " --> pdb=" O ASN X 99 " (cutoff:3.500A) Processing helix chain 'X' and resid 335 through 351 removed outlier: 4.178A pdb=" N GLU X 351 " --> pdb=" O GLU X 347 " (cutoff:3.500A) Processing helix chain 'X' and resid 475 through 479 Processing helix chain 'X' and resid 529 through 536 Processing helix chain 'X' and resid 572 through 596 Processing helix chain 'X' and resid 618 through 625 removed outlier: 3.868A pdb=" N ASN X 625 " --> pdb=" O GLU X 621 " (cutoff:3.500A) Processing helix chain 'X' and resid 627 through 636 Processing helix chain 'X' and resid 638 through 653 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.551A pdb=" N LEU E 12 " --> pdb=" O THR E 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 34 through 40 removed outlier: 4.171A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU E 45 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 95 through 99 removed outlier: 4.798A pdb=" N ARG E 96 " --> pdb=" O HIS E 100F" (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS E 100F" --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.671A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.031A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU F 46 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 495 through 499 removed outlier: 5.293A pdb=" N VAL X 608 " --> pdb=" O VAL X 36 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL X 38 " --> pdb=" O THR X 606 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR X 606 " --> pdb=" O VAL X 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 45 through 47 removed outlier: 3.629A pdb=" N ILE X 225 " --> pdb=" O VAL X 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'X' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'X' and resid 91 through 94 Processing sheet with id=AB2, first strand: chain 'X' and resid 259 through 261 removed outlier: 6.582A pdb=" N LEU X 260 " --> pdb=" O THR X 450 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N THR X 446 " --> pdb=" O VAL X 292 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N VAL X 292 " --> pdb=" O THR X 446 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N ASN X 448 " --> pdb=" O LYS X 290 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N LYS X 290 " --> pdb=" O ASN X 448 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR X 450 " --> pdb=" O LEU X 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 284 through 296 current: chain 'X' and resid 359 through 361 Processing sheet with id=AB3, first strand: chain 'X' and resid 271 through 273 removed outlier: 6.664A pdb=" N THR X 450 " --> pdb=" O LEU X 288 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N LYS X 290 " --> pdb=" O ASN X 448 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N ASN X 448 " --> pdb=" O LYS X 290 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N VAL X 292 " --> pdb=" O THR X 446 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N THR X 446 " --> pdb=" O VAL X 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 445 through 455 current: chain 'X' and resid 413 through 416 Processing sheet with id=AB4, first strand: chain 'X' and resid 374 through 378 173 hydrogen bonds defined for protein. 459 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.89 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: 1696 1.34 - 1.46: 1383 1.46 - 1.58: 2451 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 5576 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C3 BMA B 3 " pdb=" O3 BMA B 3 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" C1 NAG X 704 " pdb=" O5 NAG X 704 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C1 MAN B 5 " pdb=" C2 MAN B 5 " ideal model delta sigma weight residual 1.526 1.559 -0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 ... (remaining 5571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 7090 1.51 - 3.03: 388 3.03 - 4.54: 61 4.54 - 6.06: 11 6.06 - 7.57: 9 Bond angle restraints: 7559 Sorted by residual: angle pdb=" N ASP F 60 " pdb=" CA ASP F 60 " pdb=" C ASP F 60 " ideal model delta sigma weight residual 113.72 106.79 6.93 1.52e+00 4.33e-01 2.08e+01 angle pdb=" N ASN X 616 " pdb=" CA ASN X 616 " pdb=" C ASN X 616 " ideal model delta sigma weight residual 112.25 108.07 4.18 1.36e+00 5.41e-01 9.45e+00 angle pdb=" N ASP F 60 " pdb=" CA ASP F 60 " pdb=" CB ASP F 60 " ideal model delta sigma weight residual 113.65 109.62 4.03 1.47e+00 4.63e-01 7.51e+00 angle pdb=" N TRP X 479 " pdb=" CA TRP X 479 " pdb=" CB TRP X 479 " ideal model delta sigma weight residual 110.67 106.87 3.80 1.39e+00 5.18e-01 7.46e+00 angle pdb=" CA CYS X 247 " pdb=" CB CYS X 247 " pdb=" SG CYS X 247 " ideal model delta sigma weight residual 114.40 120.68 -6.28 2.30e+00 1.89e-01 7.45e+00 ... (remaining 7554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 3357 22.93 - 45.86: 254 45.86 - 68.80: 26 68.80 - 91.73: 21 91.73 - 114.66: 11 Dihedral angle restraints: 3669 sinusoidal: 1813 harmonic: 1856 Sorted by residual: dihedral pdb=" CB CYS X 228 " pdb=" SG CYS X 228 " pdb=" SG CYS X 239 " pdb=" CB CYS X 239 " ideal model delta sinusoidal sigma weight residual 93.00 -179.92 -87.08 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 174.15 -81.15 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CA CYS X 247 " pdb=" C CYS X 247 " pdb=" N THR X 248 " pdb=" CA THR X 248 " ideal model delta harmonic sigma weight residual -180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 3666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 873 0.108 - 0.215: 45 0.215 - 0.323: 3 0.323 - 0.431: 1 0.431 - 0.539: 1 Chirality restraints: 923 Sorted by residual: chirality pdb=" C1 NAG X 705 " pdb=" ND2 ASN X 444 " pdb=" C2 NAG X 705 " pdb=" O5 NAG X 705 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" CG LEU E 80 " pdb=" CB LEU E 80 " pdb=" CD1 LEU E 80 " pdb=" CD2 LEU E 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 920 not shown) Planarity restraints: 928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP X 479 " 0.024 2.00e-02 2.50e+03 2.45e-02 1.51e+01 pdb=" CG TRP X 479 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP X 479 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP X 479 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP X 479 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP X 479 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP X 479 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 479 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 479 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP X 479 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 13 " 0.037 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO E 14 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 60 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" CG ASP F 60 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP F 60 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP F 60 " 0.013 2.00e-02 2.50e+03 ... (remaining 925 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 480 2.74 - 3.28: 5333 3.28 - 3.82: 8470 3.82 - 4.36: 9345 4.36 - 4.90: 16057 Nonbonded interactions: 39685 Sorted by model distance: nonbonded pdb=" OG1 THR E 35 " pdb=" O GLY E 49 " model vdw 2.199 3.040 nonbonded pdb=" NH2 ARG F 61 " pdb=" O ARG F 77 " model vdw 2.246 3.120 nonbonded pdb=" OG SER F 52 " pdb=" O GLY F 64 " model vdw 2.256 3.040 nonbonded pdb=" OE2 GLU F 53 " pdb=" NH2 ARG X 500 " model vdw 2.260 3.120 nonbonded pdb=" O ALA X 525 " pdb=" OG SER X 528 " model vdw 2.282 3.040 ... (remaining 39680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'N' } 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: 1.520 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 5612 Z= 0.231 Angle : 0.849 17.193 7657 Z= 0.398 Chirality : 0.055 0.539 923 Planarity : 0.005 0.057 915 Dihedral : 16.711 114.657 2441 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.33), residues: 624 helix: 2.08 (0.51), residues: 103 sheet: -0.49 (0.36), residues: 190 loop : -1.86 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 77 TYR 0.024 0.002 TYR X 217 PHE 0.020 0.002 PHE E 78 TRP 0.066 0.003 TRP X 479 HIS 0.004 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 5576) covalent geometry : angle 0.79526 ( 7559) SS BOND : bond 0.00369 ( 10) SS BOND : angle 1.35936 ( 20) hydrogen bonds : bond 0.11152 ( 168) hydrogen bonds : angle 5.77161 ( 459) link_ALPHA1-3 : bond 0.00685 ( 2) link_ALPHA1-3 : angle 2.61020 ( 6) link_ALPHA1-6 : bond 0.00308 ( 2) link_ALPHA1-6 : angle 1.56453 ( 6) link_BETA1-4 : bond 0.00523 ( 9) link_BETA1-4 : angle 1.83066 ( 27) link_NAG-ASN : bond 0.00545 ( 13) link_NAG-ASN : angle 3.75502 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 27 GLN cc_start: 0.8616 (tm-30) cc_final: 0.7898 (tm-30) REVERT: F 83 VAL cc_start: 0.8222 (m) cc_final: 0.8015 (p) REVERT: F 90 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8369 (tm-30) REVERT: F 93 GLN cc_start: 0.8324 (pp30) cc_final: 0.8114 (pp30) REVERT: X 457 ASP cc_start: 0.7372 (t70) cc_final: 0.7139 (t0) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.0745 time to fit residues: 15.6589 Evaluate side-chains 119 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110539 restraints weight = 10422.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113960 restraints weight = 6020.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116367 restraints weight = 4290.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117974 restraints weight = 3433.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118792 restraints weight = 2959.828| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5612 Z= 0.223 Angle : 0.759 15.377 7657 Z= 0.361 Chirality : 0.050 0.479 923 Planarity : 0.005 0.050 915 Dihedral : 12.619 89.878 1224 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.33), residues: 624 helix: 2.09 (0.50), residues: 106 sheet: -0.68 (0.36), residues: 175 loop : -1.88 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 96 TYR 0.012 0.002 TYR E 32 PHE 0.016 0.002 PHE E 78 TRP 0.019 0.002 TRP X 479 HIS 0.007 0.002 HIS X 375 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 5576) covalent geometry : angle 0.69850 ( 7559) SS BOND : bond 0.00476 ( 10) SS BOND : angle 1.13186 ( 20) hydrogen bonds : bond 0.04448 ( 168) hydrogen bonds : angle 5.31787 ( 459) link_ALPHA1-3 : bond 0.00393 ( 2) link_ALPHA1-3 : angle 3.10698 ( 6) link_ALPHA1-6 : bond 0.00577 ( 2) link_ALPHA1-6 : angle 1.74542 ( 6) link_BETA1-4 : bond 0.00405 ( 9) link_BETA1-4 : angle 2.07063 ( 27) link_NAG-ASN : bond 0.00598 ( 13) link_NAG-ASN : angle 3.58087 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 9 THR cc_start: 0.7900 (p) cc_final: 0.7658 (p) REVERT: F 15 PRO cc_start: 0.8299 (Cg_endo) cc_final: 0.7818 (Cg_exo) REVERT: F 27 GLN cc_start: 0.8619 (tm-30) cc_final: 0.7968 (tm-30) REVERT: F 92 ARG cc_start: 0.8873 (tmt-80) cc_final: 0.8567 (tpt90) REVERT: F 93 GLN cc_start: 0.8463 (pp30) cc_final: 0.7670 (pp30) REVERT: X 40 TYR cc_start: 0.8578 (t80) cc_final: 0.8355 (t80) REVERT: X 280 ASN cc_start: 0.8308 (t0) cc_final: 0.7964 (t0) REVERT: X 410 PHE cc_start: 0.7281 (p90) cc_final: 0.6965 (p90) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.0792 time to fit residues: 15.0607 Evaluate side-chains 125 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 0.0030 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 375 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.144650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117728 restraints weight = 10234.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121490 restraints weight = 5929.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124078 restraints weight = 4165.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125827 restraints weight = 3286.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127019 restraints weight = 2792.521| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5612 Z= 0.123 Angle : 0.700 14.701 7657 Z= 0.330 Chirality : 0.049 0.444 923 Planarity : 0.004 0.048 915 Dihedral : 11.502 84.105 1224 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.33), residues: 624 helix: 2.08 (0.50), residues: 106 sheet: -0.52 (0.35), residues: 182 loop : -1.82 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 42 TYR 0.014 0.001 TYR X 217 PHE 0.018 0.001 PHE E 78 TRP 0.035 0.002 TRP X 479 HIS 0.003 0.001 HIS X 375 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5576) covalent geometry : angle 0.64140 ( 7559) SS BOND : bond 0.00463 ( 10) SS BOND : angle 0.98985 ( 20) hydrogen bonds : bond 0.03553 ( 168) hydrogen bonds : angle 5.01755 ( 459) link_ALPHA1-3 : bond 0.00582 ( 2) link_ALPHA1-3 : angle 3.09550 ( 6) link_ALPHA1-6 : bond 0.00498 ( 2) link_ALPHA1-6 : angle 1.72540 ( 6) link_BETA1-4 : bond 0.00470 ( 9) link_BETA1-4 : angle 1.90780 ( 27) link_NAG-ASN : bond 0.00643 ( 13) link_NAG-ASN : angle 3.40776 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 9 THR cc_start: 0.7535 (p) cc_final: 0.7292 (p) REVERT: E 20 LEU cc_start: 0.8188 (mt) cc_final: 0.7917 (mt) REVERT: E 47 TRP cc_start: 0.8773 (t60) cc_final: 0.7668 (t60) REVERT: E 75 LYS cc_start: 0.8961 (mttm) cc_final: 0.8727 (ttmm) REVERT: F 27 GLN cc_start: 0.8619 (tm-30) cc_final: 0.7919 (tm-30) REVERT: F 93 GLN cc_start: 0.8352 (pp30) cc_final: 0.8130 (pp30) REVERT: X 215 ILE cc_start: 0.8569 (tt) cc_final: 0.8260 (pt) REVERT: X 280 ASN cc_start: 0.8155 (t0) cc_final: 0.7908 (t0) REVERT: X 373 MET cc_start: 0.8974 (mmm) cc_final: 0.8484 (tpt) REVERT: X 410 PHE cc_start: 0.7289 (p90) cc_final: 0.6965 (p90) REVERT: X 457 ASP cc_start: 0.7615 (t70) cc_final: 0.7395 (t0) REVERT: X 568 MET cc_start: 0.6764 (tmm) cc_final: 0.6476 (tmm) REVERT: X 614 TRP cc_start: 0.8772 (m-10) cc_final: 0.8319 (m-90) outliers start: 1 outliers final: 1 residues processed: 166 average time/residue: 0.0654 time to fit residues: 14.1576 Evaluate side-chains 131 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.0970 chunk 4 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.146145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118791 restraints weight = 10345.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122437 restraints weight = 6000.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124950 restraints weight = 4264.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126528 restraints weight = 3414.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127720 restraints weight = 2958.292| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5612 Z= 0.117 Angle : 0.689 14.174 7657 Z= 0.322 Chirality : 0.049 0.431 923 Planarity : 0.004 0.046 915 Dihedral : 10.350 69.108 1224 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.35 % Allowed : 2.63 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.33), residues: 624 helix: 2.26 (0.51), residues: 106 sheet: -0.35 (0.36), residues: 177 loop : -1.84 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 500 TYR 0.014 0.001 TYR X 486 PHE 0.014 0.001 PHE E 78 TRP 0.033 0.001 TRP X 479 HIS 0.006 0.001 HIS X 216 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5576) covalent geometry : angle 0.63075 ( 7559) SS BOND : bond 0.00712 ( 10) SS BOND : angle 0.93752 ( 20) hydrogen bonds : bond 0.03305 ( 168) hydrogen bonds : angle 4.81491 ( 459) link_ALPHA1-3 : bond 0.00698 ( 2) link_ALPHA1-3 : angle 3.18222 ( 6) link_ALPHA1-6 : bond 0.00501 ( 2) link_ALPHA1-6 : angle 1.81822 ( 6) link_BETA1-4 : bond 0.00427 ( 9) link_BETA1-4 : angle 1.94756 ( 27) link_NAG-ASN : bond 0.00603 ( 13) link_NAG-ASN : angle 3.29378 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 LEU cc_start: 0.8576 (mm) cc_final: 0.8353 (mm) REVERT: E 9 THR cc_start: 0.7423 (p) cc_final: 0.7198 (p) REVERT: E 20 LEU cc_start: 0.8207 (mt) cc_final: 0.7919 (mt) REVERT: E 47 TRP cc_start: 0.8704 (t60) cc_final: 0.7567 (t60) REVERT: F 27 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7305 (tm-30) REVERT: F 83 VAL cc_start: 0.8529 (m) cc_final: 0.8328 (p) REVERT: F 92 ARG cc_start: 0.8762 (tpt90) cc_final: 0.8485 (tpt-90) REVERT: X 215 ILE cc_start: 0.8696 (tt) cc_final: 0.8346 (pt) REVERT: X 410 PHE cc_start: 0.7240 (p90) cc_final: 0.6912 (p90) REVERT: X 457 ASP cc_start: 0.7573 (t70) cc_final: 0.7353 (t0) outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.0715 time to fit residues: 14.5228 Evaluate side-chains 128 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 0.0010 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118824 restraints weight = 10417.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122515 restraints weight = 6079.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125044 restraints weight = 4344.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126593 restraints weight = 3481.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.127823 restraints weight = 3016.136| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5612 Z= 0.113 Angle : 0.663 13.884 7657 Z= 0.313 Chirality : 0.048 0.422 923 Planarity : 0.004 0.045 915 Dihedral : 8.972 63.459 1224 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.18 % Allowed : 2.80 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.33), residues: 624 helix: 2.24 (0.51), residues: 106 sheet: -0.34 (0.37), residues: 174 loop : -1.80 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 100E TYR 0.014 0.001 TYR X 486 PHE 0.012 0.001 PHE E 78 TRP 0.031 0.002 TRP X 479 HIS 0.004 0.001 HIS X 375 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5576) covalent geometry : angle 0.60369 ( 7559) SS BOND : bond 0.00336 ( 10) SS BOND : angle 0.95439 ( 20) hydrogen bonds : bond 0.03138 ( 168) hydrogen bonds : angle 4.74043 ( 459) link_ALPHA1-3 : bond 0.00652 ( 2) link_ALPHA1-3 : angle 3.25027 ( 6) link_ALPHA1-6 : bond 0.00463 ( 2) link_ALPHA1-6 : angle 1.89812 ( 6) link_BETA1-4 : bond 0.00436 ( 9) link_BETA1-4 : angle 2.03400 ( 27) link_NAG-ASN : bond 0.00615 ( 13) link_NAG-ASN : angle 3.19121 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: E 9 THR cc_start: 0.7325 (p) cc_final: 0.7105 (p) REVERT: E 20 LEU cc_start: 0.8231 (mt) cc_final: 0.7897 (mt) REVERT: E 47 TRP cc_start: 0.8682 (t60) cc_final: 0.7524 (t60) REVERT: E 87 MET cc_start: 0.7353 (tpp) cc_final: 0.7028 (mmm) REVERT: F 27 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7890 (tm-30) REVERT: F 90 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8323 (tm-30) REVERT: X 215 ILE cc_start: 0.8685 (tt) cc_final: 0.8374 (pt) REVERT: X 280 ASN cc_start: 0.8444 (t0) cc_final: 0.8125 (t0) REVERT: X 373 MET cc_start: 0.9006 (mmm) cc_final: 0.8641 (tpt) REVERT: X 410 PHE cc_start: 0.7270 (p90) cc_final: 0.6923 (p90) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.0628 time to fit residues: 13.2030 Evaluate side-chains 128 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 375 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115371 restraints weight = 10339.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118893 restraints weight = 6130.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121280 restraints weight = 4439.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122887 restraints weight = 3599.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123731 restraints weight = 3123.840| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5612 Z= 0.160 Angle : 0.696 13.914 7657 Z= 0.333 Chirality : 0.049 0.446 923 Planarity : 0.004 0.041 915 Dihedral : 8.744 59.026 1224 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.18 % Allowed : 2.45 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.33), residues: 624 helix: 2.21 (0.51), residues: 106 sheet: -0.51 (0.37), residues: 179 loop : -1.77 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 69 TYR 0.013 0.002 TYR X 40 PHE 0.012 0.001 PHE E 78 TRP 0.041 0.002 TRP X 479 HIS 0.003 0.001 HIS X 287 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5576) covalent geometry : angle 0.64088 ( 7559) SS BOND : bond 0.00441 ( 10) SS BOND : angle 1.35250 ( 20) hydrogen bonds : bond 0.03540 ( 168) hydrogen bonds : angle 4.83986 ( 459) link_ALPHA1-3 : bond 0.00491 ( 2) link_ALPHA1-3 : angle 3.28666 ( 6) link_ALPHA1-6 : bond 0.00435 ( 2) link_ALPHA1-6 : angle 1.89499 ( 6) link_BETA1-4 : bond 0.00380 ( 9) link_BETA1-4 : angle 1.56925 ( 27) link_NAG-ASN : bond 0.00614 ( 13) link_NAG-ASN : angle 3.25623 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.215 Fit side-chains REVERT: E 20 LEU cc_start: 0.8467 (mt) cc_final: 0.8168 (mt) REVERT: E 47 TRP cc_start: 0.8703 (t60) cc_final: 0.7526 (t60) REVERT: E 64 ARG cc_start: 0.8422 (ttt90) cc_final: 0.8193 (ttm-80) REVERT: F 27 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7759 (tm-30) REVERT: X 280 ASN cc_start: 0.8572 (t0) cc_final: 0.8172 (t0) REVERT: X 410 PHE cc_start: 0.7353 (p90) cc_final: 0.7042 (p90) outliers start: 1 outliers final: 1 residues processed: 156 average time/residue: 0.0589 time to fit residues: 12.1360 Evaluate side-chains 117 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116933 restraints weight = 10522.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120572 restraints weight = 6226.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123063 restraints weight = 4453.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124712 restraints weight = 3567.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125718 restraints weight = 3080.170| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5612 Z= 0.143 Angle : 0.713 13.632 7657 Z= 0.343 Chirality : 0.049 0.433 923 Planarity : 0.004 0.051 915 Dihedral : 8.409 55.880 1224 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.18 % Allowed : 0.88 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.33), residues: 624 helix: 2.25 (0.51), residues: 106 sheet: -0.49 (0.37), residues: 174 loop : -1.81 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 42 TYR 0.019 0.002 TYR X 217 PHE 0.017 0.001 PHE E 78 TRP 0.038 0.002 TRP X 479 HIS 0.004 0.001 HIS X 375 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5576) covalent geometry : angle 0.66101 ( 7559) SS BOND : bond 0.00429 ( 10) SS BOND : angle 1.33439 ( 20) hydrogen bonds : bond 0.03496 ( 168) hydrogen bonds : angle 4.81269 ( 459) link_ALPHA1-3 : bond 0.00620 ( 2) link_ALPHA1-3 : angle 3.29400 ( 6) link_ALPHA1-6 : bond 0.00478 ( 2) link_ALPHA1-6 : angle 1.92917 ( 6) link_BETA1-4 : bond 0.00430 ( 9) link_BETA1-4 : angle 1.63463 ( 27) link_NAG-ASN : bond 0.00589 ( 13) link_NAG-ASN : angle 3.17132 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: E 9 THR cc_start: 0.7600 (p) cc_final: 0.7390 (p) REVERT: E 20 LEU cc_start: 0.8415 (mt) cc_final: 0.8140 (mt) REVERT: E 64 ARG cc_start: 0.8370 (ttt90) cc_final: 0.8130 (ttm-80) REVERT: E 87 MET cc_start: 0.7554 (tpp) cc_final: 0.6602 (mmm) REVERT: F 27 GLN cc_start: 0.8542 (tm-30) cc_final: 0.7797 (tm-30) REVERT: X 280 ASN cc_start: 0.8492 (t0) cc_final: 0.8143 (t0) REVERT: X 373 MET cc_start: 0.9041 (mmm) cc_final: 0.8593 (tpt) REVERT: X 410 PHE cc_start: 0.7296 (p90) cc_final: 0.6996 (p90) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.0692 time to fit residues: 14.1226 Evaluate side-chains 122 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.0050 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 246 GLN X 283 ASN X 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117527 restraints weight = 10509.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121150 restraints weight = 6181.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123624 restraints weight = 4431.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125315 restraints weight = 3554.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126325 restraints weight = 3063.315| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5612 Z= 0.131 Angle : 0.702 13.478 7657 Z= 0.337 Chirality : 0.049 0.429 923 Planarity : 0.004 0.048 915 Dihedral : 8.072 54.140 1224 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.35 % Allowed : 1.40 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.33), residues: 624 helix: 2.37 (0.51), residues: 103 sheet: -0.58 (0.37), residues: 189 loop : -1.79 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 42 TYR 0.017 0.002 TYR X 486 PHE 0.015 0.001 PHE E 78 TRP 0.043 0.002 TRP X 479 HIS 0.003 0.001 HIS X 375 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5576) covalent geometry : angle 0.65170 ( 7559) SS BOND : bond 0.00607 ( 10) SS BOND : angle 1.34891 ( 20) hydrogen bonds : bond 0.03374 ( 168) hydrogen bonds : angle 4.79612 ( 459) link_ALPHA1-3 : bond 0.00568 ( 2) link_ALPHA1-3 : angle 3.25595 ( 6) link_ALPHA1-6 : bond 0.00528 ( 2) link_ALPHA1-6 : angle 1.94318 ( 6) link_BETA1-4 : bond 0.00397 ( 9) link_BETA1-4 : angle 1.58017 ( 27) link_NAG-ASN : bond 0.00582 ( 13) link_NAG-ASN : angle 3.09221 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: E 20 LEU cc_start: 0.8461 (mt) cc_final: 0.8193 (mt) REVERT: E 47 TRP cc_start: 0.8684 (t60) cc_final: 0.7485 (t60) REVERT: E 87 MET cc_start: 0.7991 (tpp) cc_final: 0.7062 (mmm) REVERT: F 27 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7762 (tm-30) REVERT: X 102 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7492 (pp20) REVERT: X 280 ASN cc_start: 0.8421 (t0) cc_final: 0.8085 (t0) REVERT: X 373 MET cc_start: 0.9097 (mmm) cc_final: 0.8664 (tpt) REVERT: X 410 PHE cc_start: 0.7300 (p90) cc_final: 0.7002 (p90) outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.0651 time to fit residues: 13.0141 Evaluate side-chains 126 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 283 ASN X 375 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.145327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117176 restraints weight = 10370.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120824 restraints weight = 6140.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123288 restraints weight = 4427.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124541 restraints weight = 3573.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125957 restraints weight = 3143.440| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5612 Z= 0.143 Angle : 0.724 13.353 7657 Z= 0.345 Chirality : 0.049 0.428 923 Planarity : 0.004 0.042 915 Dihedral : 7.953 53.071 1224 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.33), residues: 624 helix: 2.30 (0.51), residues: 103 sheet: -0.40 (0.37), residues: 174 loop : -1.88 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 77 TYR 0.018 0.002 TYR E 91 PHE 0.018 0.001 PHE E 78 TRP 0.044 0.002 TRP X 479 HIS 0.008 0.001 HIS X 375 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5576) covalent geometry : angle 0.67403 ( 7559) SS BOND : bond 0.00480 ( 10) SS BOND : angle 1.19719 ( 20) hydrogen bonds : bond 0.03412 ( 168) hydrogen bonds : angle 4.83233 ( 459) link_ALPHA1-3 : bond 0.00642 ( 2) link_ALPHA1-3 : angle 3.26182 ( 6) link_ALPHA1-6 : bond 0.00548 ( 2) link_ALPHA1-6 : angle 1.96435 ( 6) link_BETA1-4 : bond 0.00389 ( 9) link_BETA1-4 : angle 1.61293 ( 27) link_NAG-ASN : bond 0.00660 ( 13) link_NAG-ASN : angle 3.16033 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: E 3 GLN cc_start: 0.7611 (mt0) cc_final: 0.7338 (mt0) REVERT: E 47 TRP cc_start: 0.8691 (t60) cc_final: 0.7525 (t60) REVERT: F 27 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7759 (tm-30) REVERT: X 102 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7517 (pp20) REVERT: X 280 ASN cc_start: 0.8397 (t0) cc_final: 0.8080 (t0) REVERT: X 410 PHE cc_start: 0.7319 (p90) cc_final: 0.7023 (p90) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.0698 time to fit residues: 14.2241 Evaluate side-chains 122 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.146614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118618 restraints weight = 10329.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122346 restraints weight = 6041.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124767 restraints weight = 4291.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126462 restraints weight = 3455.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127448 restraints weight = 2982.415| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5612 Z= 0.132 Angle : 0.720 13.248 7657 Z= 0.347 Chirality : 0.049 0.427 923 Planarity : 0.004 0.042 915 Dihedral : 7.781 52.005 1224 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.33), residues: 624 helix: 2.47 (0.51), residues: 103 sheet: -0.35 (0.38), residues: 174 loop : -1.84 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 77 TYR 0.019 0.002 TYR E 91 PHE 0.020 0.001 PHE F 96 TRP 0.038 0.002 TRP X 479 HIS 0.002 0.001 HIS X 287 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5576) covalent geometry : angle 0.67300 ( 7559) SS BOND : bond 0.00463 ( 10) SS BOND : angle 1.29786 ( 20) hydrogen bonds : bond 0.03318 ( 168) hydrogen bonds : angle 4.77812 ( 459) link_ALPHA1-3 : bond 0.00657 ( 2) link_ALPHA1-3 : angle 3.27404 ( 6) link_ALPHA1-6 : bond 0.00560 ( 2) link_ALPHA1-6 : angle 1.97412 ( 6) link_BETA1-4 : bond 0.00417 ( 9) link_BETA1-4 : angle 1.54280 ( 27) link_NAG-ASN : bond 0.00590 ( 13) link_NAG-ASN : angle 3.04727 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: E 3 GLN cc_start: 0.7615 (mt0) cc_final: 0.7348 (mt0) REVERT: E 47 TRP cc_start: 0.8565 (t60) cc_final: 0.7366 (t60) REVERT: F 27 GLN cc_start: 0.8612 (tm-30) cc_final: 0.7779 (tm-30) REVERT: X 102 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7521 (pp20) REVERT: X 280 ASN cc_start: 0.8294 (t0) cc_final: 0.7992 (t0) REVERT: X 410 PHE cc_start: 0.7376 (p90) cc_final: 0.7070 (p90) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.0610 time to fit residues: 12.4497 Evaluate side-chains 120 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 58 optimal weight: 0.0870 chunk 55 optimal weight: 0.0170 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120366 restraints weight = 10217.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124099 restraints weight = 5965.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126667 restraints weight = 4229.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128350 restraints weight = 3381.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129377 restraints weight = 2904.572| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5612 Z= 0.131 Angle : 0.721 13.077 7657 Z= 0.349 Chirality : 0.049 0.423 923 Planarity : 0.004 0.044 915 Dihedral : 7.601 50.875 1224 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.34), residues: 624 helix: 2.60 (0.51), residues: 103 sheet: -0.37 (0.38), residues: 174 loop : -1.82 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 96 TYR 0.021 0.002 TYR E 91 PHE 0.016 0.001 PHE E 78 TRP 0.036 0.002 TRP X 479 HIS 0.002 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5576) covalent geometry : angle 0.67518 ( 7559) SS BOND : bond 0.00399 ( 10) SS BOND : angle 1.24263 ( 20) hydrogen bonds : bond 0.03274 ( 168) hydrogen bonds : angle 4.72381 ( 459) link_ALPHA1-3 : bond 0.00638 ( 2) link_ALPHA1-3 : angle 3.22689 ( 6) link_ALPHA1-6 : bond 0.00579 ( 2) link_ALPHA1-6 : angle 1.97685 ( 6) link_BETA1-4 : bond 0.00374 ( 9) link_BETA1-4 : angle 1.52856 ( 27) link_NAG-ASN : bond 0.00567 ( 13) link_NAG-ASN : angle 3.00471 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 977.60 seconds wall clock time: 17 minutes 31.16 seconds (1051.16 seconds total)