Starting phenix.real_space_refine on Thu Mar 6 09:10:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gp5_34190/03_2025/8gp5_34190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gp5_34190/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gp5_34190/03_2025/8gp5_34190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gp5_34190/03_2025/8gp5_34190.map" model { file = "/net/cci-nas-00/data/ceres_data/8gp5_34190/03_2025/8gp5_34190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gp5_34190/03_2025/8gp5_34190.cif" } resolution = 4.05 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= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.07, per 1000 atoms: 0.74 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: 1.57 Conformation dependent library (CDL) restraints added in 699.3 milliseconds 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: 0.63 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: 1.62 Time building geometry restraints manager: 1.84 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: 1.440 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.580 ------------------------------------------------------------------------------- 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 5576 Z= 0.287 Angle : 0.795 7.572 7559 Z= 0.386 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 (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: -1.09 (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 TRP 0.066 0.003 TRP X 479 HIS 0.004 0.001 HIS X 374 PHE 0.020 0.002 PHE E 78 TYR 0.024 0.002 TYR X 217 ARG 0.005 0.001 ARG F 77 *********************** 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 : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 9 THR cc_start: 0.7595 (p) cc_final: 0.7391 (p) REVERT: F 27 GLN cc_start: 0.8616 (tm-30) cc_final: 0.7899 (tm-30) REVERT: F 83 VAL cc_start: 0.8222 (m) cc_final: 0.8017 (p) REVERT: F 90 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8367 (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: 0.1805 time to fit residues: 37.7728 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 : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 X 258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.144828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117599 restraints weight = 10187.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121239 restraints weight = 5969.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123645 restraints weight = 4245.688| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5576 Z= 0.210 Angle : 0.633 9.705 7559 Z= 0.317 Chirality : 0.049 0.456 923 Planarity : 0.004 0.049 915 Dihedral : 12.555 93.684 1224 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.09 (0.33), residues: 624 helix: 2.12 (0.51), residues: 106 sheet: -0.54 (0.36), residues: 177 loop : -1.83 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 479 HIS 0.004 0.001 HIS X 375 PHE 0.014 0.001 PHE E 78 TYR 0.011 0.001 TYR E 91 ARG 0.006 0.001 ARG E 96 *********************** 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 155 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: E 9 THR cc_start: 0.7636 (p) cc_final: 0.7426 (p) REVERT: E 20 LEU cc_start: 0.8257 (mt) cc_final: 0.7955 (mt) REVERT: F 6 GLN cc_start: 0.7940 (mt0) cc_final: 0.7349 (mt0) REVERT: F 27 GLN cc_start: 0.8592 (tm-30) cc_final: 0.7928 (tm-30) REVERT: F 93 GLN cc_start: 0.8462 (pp30) cc_final: 0.7984 (pp30) REVERT: X 280 ASN cc_start: 0.8280 (t0) cc_final: 0.7942 (t0) REVERT: X 410 PHE cc_start: 0.7245 (p90) cc_final: 0.7016 (p90) REVERT: X 568 MET cc_start: 0.6688 (tmm) cc_final: 0.6342 (tmm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1764 time to fit residues: 34.8098 Evaluate side-chains 126 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 258 GLN X 375 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117637 restraints weight = 10262.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121214 restraints weight = 6014.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123692 restraints weight = 4296.782| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 5576 Z= 0.221 Angle : 0.644 10.913 7559 Z= 0.322 Chirality : 0.049 0.437 923 Planarity : 0.004 0.046 915 Dihedral : 11.601 84.984 1224 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.18 % Allowed : 3.33 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.06 (0.33), residues: 624 helix: 2.15 (0.51), residues: 106 sheet: -0.57 (0.36), residues: 182 loop : -1.80 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP X 479 HIS 0.003 0.001 HIS X 375 PHE 0.017 0.001 PHE E 78 TYR 0.013 0.001 TYR X 40 ARG 0.005 0.000 ARG E 66 *********************** 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 160 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.473 Fit side-chains REVERT: E 9 THR cc_start: 0.7529 (p) cc_final: 0.7296 (p) REVERT: E 20 LEU cc_start: 0.8242 (mt) cc_final: 0.7930 (mt) REVERT: E 47 TRP cc_start: 0.8772 (t60) cc_final: 0.8430 (t60) REVERT: F 27 GLN cc_start: 0.8674 (tm-30) cc_final: 0.7912 (tm-30) REVERT: X 280 ASN cc_start: 0.8195 (t0) cc_final: 0.7862 (t0) REVERT: X 410 PHE cc_start: 0.7246 (p90) cc_final: 0.6941 (p90) REVERT: X 457 ASP cc_start: 0.7586 (t70) cc_final: 0.7362 (t0) REVERT: X 479 TRP cc_start: 0.7980 (m-10) cc_final: 0.7601 (m-10) outliers start: 1 outliers final: 1 residues processed: 159 average time/residue: 0.1858 time to fit residues: 37.3999 Evaluate side-chains 120 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.0370 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.145118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117358 restraints weight = 10541.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121125 restraints weight = 6070.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.123690 restraints weight = 4312.906| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5576 Z= 0.180 Angle : 0.632 11.986 7559 Z= 0.312 Chirality : 0.048 0.424 923 Planarity : 0.004 0.045 915 Dihedral : 10.555 70.477 1224 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.02 (0.33), residues: 624 helix: 2.25 (0.51), residues: 106 sheet: -0.43 (0.36), residues: 177 loop : -1.84 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP X 479 HIS 0.006 0.001 HIS X 375 PHE 0.014 0.001 PHE E 78 TYR 0.013 0.001 TYR X 40 ARG 0.004 0.001 ARG E 96 *********************** 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 154 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: E 4 LEU cc_start: 0.8564 (mm) cc_final: 0.8358 (mm) REVERT: E 20 LEU cc_start: 0.8261 (mt) cc_final: 0.7910 (mt) REVERT: E 47 TRP cc_start: 0.8709 (t60) cc_final: 0.7540 (t60) REVERT: F 27 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7614 (tm-30) REVERT: X 102 GLU cc_start: 0.7440 (pp20) cc_final: 0.7197 (pp20) REVERT: X 280 ASN cc_start: 0.8197 (t0) cc_final: 0.7916 (t0) REVERT: X 410 PHE cc_start: 0.7280 (p90) cc_final: 0.6961 (p90) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1814 time to fit residues: 36.2161 Evaluate side-chains 129 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 0.0470 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 54 optimal weight: 0.0070 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.146316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118859 restraints weight = 10390.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122561 restraints weight = 6034.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125053 restraints weight = 4290.851| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5576 Z= 0.176 Angle : 0.625 9.763 7559 Z= 0.310 Chirality : 0.048 0.419 923 Planarity : 0.004 0.044 915 Dihedral : 9.264 64.665 1224 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.05 (0.33), residues: 624 helix: 2.24 (0.50), residues: 106 sheet: -0.47 (0.37), residues: 174 loop : -1.85 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP X 479 HIS 0.004 0.001 HIS X 375 PHE 0.012 0.001 PHE E 78 TYR 0.013 0.002 TYR X 217 ARG 0.003 0.000 ARG F 24 *********************** 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 154 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: E 9 THR cc_start: 0.7362 (p) cc_final: 0.7126 (p) REVERT: E 20 LEU cc_start: 0.8270 (mt) cc_final: 0.7890 (mt) REVERT: E 47 TRP cc_start: 0.8727 (t60) cc_final: 0.7591 (t60) REVERT: F 27 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7786 (tm-30) REVERT: X 280 ASN cc_start: 0.8562 (t0) cc_final: 0.8269 (t0) REVERT: X 373 MET cc_start: 0.8279 (tpp) cc_final: 0.7989 (tpp) REVERT: X 410 PHE cc_start: 0.7267 (p90) cc_final: 0.6936 (p90) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1689 time to fit residues: 33.5748 Evaluate side-chains 123 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 0.0270 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.144446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116699 restraints weight = 10384.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120323 restraints weight = 6106.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122718 restraints weight = 4375.067| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5576 Z= 0.212 Angle : 0.628 6.720 7559 Z= 0.315 Chirality : 0.048 0.428 923 Planarity : 0.004 0.043 915 Dihedral : 8.773 59.469 1224 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.09 (0.33), residues: 624 helix: 2.22 (0.51), residues: 106 sheet: -0.54 (0.37), residues: 174 loop : -1.86 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP X 479 HIS 0.003 0.001 HIS X 375 PHE 0.012 0.001 PHE E 78 TYR 0.019 0.002 TYR X 217 ARG 0.004 0.001 ARG F 77 *********************** 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 154 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.556 Fit side-chains REVERT: E 20 LEU cc_start: 0.8383 (mt) cc_final: 0.8060 (mt) REVERT: E 47 TRP cc_start: 0.8751 (t60) cc_final: 0.7559 (t60) REVERT: F 27 GLN cc_start: 0.8506 (tm-30) cc_final: 0.7866 (tm-30) REVERT: X 102 GLU cc_start: 0.7268 (pp20) cc_final: 0.7045 (pp20) REVERT: X 280 ASN cc_start: 0.8508 (t0) cc_final: 0.8123 (t0) REVERT: X 373 MET cc_start: 0.8399 (tpp) cc_final: 0.7790 (tpt) REVERT: X 410 PHE cc_start: 0.7315 (p90) cc_final: 0.6983 (p90) REVERT: X 457 ASP cc_start: 0.7380 (t70) cc_final: 0.7177 (t0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1542 time to fit residues: 31.2969 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 : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.143974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115962 restraints weight = 10323.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119466 restraints weight = 6088.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121918 restraints weight = 4399.761| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5576 Z= 0.241 Angle : 0.659 7.511 7559 Z= 0.328 Chirality : 0.050 0.439 923 Planarity : 0.004 0.043 915 Dihedral : 8.491 55.948 1224 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.18 % Allowed : 1.58 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.19 (0.33), residues: 624 helix: 2.16 (0.50), residues: 106 sheet: -0.66 (0.37), residues: 172 loop : -1.89 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP X 479 HIS 0.003 0.001 HIS X 375 PHE 0.018 0.001 PHE E 78 TYR 0.024 0.002 TYR X 217 ARG 0.004 0.001 ARG F 42 *********************** 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 158 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.564 Fit side-chains REVERT: E 9 THR cc_start: 0.7693 (p) cc_final: 0.7487 (p) REVERT: E 20 LEU cc_start: 0.8404 (mt) cc_final: 0.8090 (mt) REVERT: E 47 TRP cc_start: 0.8759 (t60) cc_final: 0.7662 (t60) REVERT: F 27 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7858 (tm-30) REVERT: X 102 GLU cc_start: 0.7275 (pp20) cc_final: 0.7055 (pp20) REVERT: X 280 ASN cc_start: 0.8514 (t0) cc_final: 0.8139 (t0) REVERT: X 410 PHE cc_start: 0.7233 (p90) cc_final: 0.6935 (p90) REVERT: X 457 ASP cc_start: 0.7385 (t70) cc_final: 0.7181 (t0) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.1676 time to fit residues: 34.1779 Evaluate side-chains 121 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 0.0170 chunk 20 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 53 optimal weight: 6.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114952 restraints weight = 10351.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118618 restraints weight = 6076.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121061 restraints weight = 4341.776| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5576 Z= 0.226 Angle : 0.689 8.016 7559 Z= 0.344 Chirality : 0.050 0.444 923 Planarity : 0.004 0.042 915 Dihedral : 8.310 54.568 1224 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.15 (0.33), residues: 624 helix: 2.21 (0.51), residues: 106 sheet: -0.62 (0.37), residues: 174 loop : -1.89 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP X 479 HIS 0.005 0.001 HIS X 375 PHE 0.017 0.001 PHE E 78 TYR 0.025 0.002 TYR X 217 ARG 0.005 0.001 ARG X 379 *********************** 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 151 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: E 47 TRP cc_start: 0.8763 (t60) cc_final: 0.7650 (t60) REVERT: F 27 GLN cc_start: 0.8524 (tm-30) cc_final: 0.7814 (tm-30) REVERT: X 280 ASN cc_start: 0.8378 (t0) cc_final: 0.8081 (t0) REVERT: X 410 PHE cc_start: 0.7251 (p90) cc_final: 0.6957 (p90) REVERT: X 457 ASP cc_start: 0.7440 (t70) cc_final: 0.7234 (t0) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1580 time to fit residues: 31.3650 Evaluate side-chains 117 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.144107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116056 restraints weight = 10243.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119677 restraints weight = 6044.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.122155 restraints weight = 4351.043| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5576 Z= 0.233 Angle : 0.696 8.602 7559 Z= 0.346 Chirality : 0.050 0.438 923 Planarity : 0.004 0.043 915 Dihedral : 8.172 53.520 1224 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.18 (0.33), residues: 624 helix: 2.12 (0.51), residues: 106 sheet: -0.59 (0.37), residues: 174 loop : -1.92 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP X 479 HIS 0.006 0.001 HIS X 375 PHE 0.017 0.001 PHE E 78 TYR 0.028 0.002 TYR X 217 ARG 0.005 0.001 ARG X 379 *********************** 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 149 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: E 47 TRP cc_start: 0.8747 (t60) cc_final: 0.7753 (t60) REVERT: F 27 GLN cc_start: 0.8552 (tm-30) cc_final: 0.7790 (tm-30) REVERT: X 102 GLU cc_start: 0.7266 (pp20) cc_final: 0.7052 (pp20) REVERT: X 280 ASN cc_start: 0.8354 (t0) cc_final: 0.8086 (t0) REVERT: X 410 PHE cc_start: 0.7267 (p90) cc_final: 0.6964 (p90) REVERT: X 457 ASP cc_start: 0.7432 (t70) cc_final: 0.7229 (t0) REVERT: X 626 MET cc_start: 0.6906 (ttm) cc_final: 0.6182 (ttp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1672 time to fit residues: 32.4416 Evaluate side-chains 118 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116307 restraints weight = 10328.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120018 restraints weight = 6091.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122572 restraints weight = 4349.829| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 5576 Z= 0.263 Angle : 0.717 8.972 7559 Z= 0.358 Chirality : 0.050 0.443 923 Planarity : 0.004 0.044 915 Dihedral : 8.149 52.662 1224 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.18 (0.33), residues: 624 helix: 2.39 (0.52), residues: 103 sheet: -0.61 (0.37), residues: 184 loop : -2.00 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP X 479 HIS 0.006 0.001 HIS X 375 PHE 0.017 0.001 PHE E 78 TYR 0.028 0.002 TYR X 217 ARG 0.005 0.001 ARG E 96 ********************** 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 150 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 TRP cc_start: 0.8762 (t60) cc_final: 0.7704 (t60) REVERT: E 87 MET cc_start: 0.8251 (tpp) cc_final: 0.7776 (tpp) REVERT: F 27 GLN cc_start: 0.8598 (tm-30) cc_final: 0.7806 (tm-30) REVERT: X 102 GLU cc_start: 0.7266 (pp20) cc_final: 0.7056 (pp20) REVERT: X 104 MET cc_start: 0.8572 (tmm) cc_final: 0.8338 (tmm) REVERT: X 280 ASN cc_start: 0.8260 (t0) cc_final: 0.8037 (t0) REVERT: X 410 PHE cc_start: 0.7114 (p90) cc_final: 0.6862 (p90) REVERT: X 457 ASP cc_start: 0.7451 (t70) cc_final: 0.7238 (t0) REVERT: X 614 TRP cc_start: 0.8830 (m-10) cc_final: 0.8421 (m-90) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1701 time to fit residues: 33.0453 Evaluate side-chains 118 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 45 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118494 restraints weight = 10350.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122312 restraints weight = 6025.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124875 restraints weight = 4263.494| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5576 Z= 0.193 Angle : 0.696 8.004 7559 Z= 0.348 Chirality : 0.050 0.436 923 Planarity : 0.004 0.046 915 Dihedral : 7.861 51.123 1224 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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 (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 (0.33), residues: 624 helix: 2.42 (0.52), residues: 103 sheet: -0.53 (0.37), residues: 174 loop : -1.91 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP X 479 HIS 0.005 0.001 HIS X 375 PHE 0.017 0.001 PHE F 96 TYR 0.023 0.002 TYR X 217 ARG 0.005 0.001 ARG X 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.63 seconds wall clock time: 35 minutes 46.29 seconds (2146.29 seconds total)