Starting phenix.real_space_refine on Sun Mar 10 22:01:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp5_34190/03_2024/8gp5_34190.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp5_34190/03_2024/8gp5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp5_34190/03_2024/8gp5_34190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp5_34190/03_2024/8gp5_34190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp5_34190/03_2024/8gp5_34190.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp5_34190/03_2024/8gp5_34190.pdb" } 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 Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "F ASP 30": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 275": "OE1" <-> "OE2" Residue "X GLU 332": "OE1" <-> "OE2" Residue "X PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 466": "OE1" <-> "OE2" Residue "X TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.67, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 2.85 Conformation dependent library (CDL) restraints added in 948.8 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: 0.65 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: 1.53 Time building geometry restraints manager: 3.02 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: 98.05 - 105.24: 84 105.24 - 112.42: 3021 112.42 - 119.61: 1785 119.61 - 126.80: 2575 126.80 - 133.99: 94 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 2.440 nonbonded pdb=" NH2 ARG F 61 " pdb=" O ARG F 77 " model vdw 2.246 2.520 nonbonded pdb=" OG SER F 52 " pdb=" O GLY F 64 " model vdw 2.256 2.440 nonbonded pdb=" OE2 GLU F 53 " pdb=" NH2 ARG X 500 " model vdw 2.260 2.520 nonbonded pdb=" O ALA X 525 " pdb=" OG SER X 528 " model vdw 2.282 2.440 ... (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 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: 1.020 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: 4.750 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.490 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 0.577 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: 0.1828 time to fit residues: 37.9484 Evaluate side-chains 120 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 0.3980 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.0060 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5576 Z= 0.191 Angle : 0.611 9.647 7559 Z= 0.305 Chirality : 0.048 0.448 923 Planarity : 0.004 0.049 915 Dihedral : 12.766 91.357 1224 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % 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: 2.17 (0.52), residues: 105 sheet: -0.50 (0.36), residues: 177 loop : -1.82 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 479 HIS 0.008 0.002 HIS X 375 PHE 0.015 0.001 PHE E 78 TYR 0.012 0.001 TYR E 91 ARG 0.005 0.000 ARG F 92 *********************** 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 fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 9 THR cc_start: 0.7636 (p) cc_final: 0.7386 (p) REVERT: E 20 LEU cc_start: 0.8220 (mt) cc_final: 0.7907 (mt) REVERT: F 27 GLN cc_start: 0.8606 (tm-30) cc_final: 0.7984 (tm-30) REVERT: F 93 GLN cc_start: 0.8453 (pp30) cc_final: 0.7978 (pp30) REVERT: X 410 PHE cc_start: 0.7252 (p90) cc_final: 0.7004 (p90) REVERT: X 568 MET cc_start: 0.6643 (tmm) cc_final: 0.6281 (tmm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1807 time to fit residues: 35.8529 Evaluate side-chains 130 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 48 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5576 Z= 0.187 Angle : 0.620 11.257 7559 Z= 0.306 Chirality : 0.048 0.448 923 Planarity : 0.004 0.047 915 Dihedral : 11.626 77.959 1224 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % 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: -1.03 (0.33), residues: 624 helix: 2.06 (0.51), residues: 106 sheet: -0.50 (0.36), residues: 182 loop : -1.77 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP X 479 HIS 0.005 0.001 HIS X 216 PHE 0.017 0.001 PHE E 78 TYR 0.013 0.001 TYR X 40 ARG 0.006 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 fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 9 THR cc_start: 0.7520 (p) cc_final: 0.7297 (p) REVERT: E 20 LEU cc_start: 0.8179 (mt) cc_final: 0.7842 (mt) REVERT: F 27 GLN cc_start: 0.8700 (tm-30) cc_final: 0.7933 (tm-30) REVERT: X 410 PHE cc_start: 0.7237 (p90) cc_final: 0.6929 (p90) REVERT: X 457 ASP cc_start: 0.7526 (t70) cc_final: 0.7299 (t0) outliers start: 1 outliers final: 1 residues processed: 159 average time/residue: 0.1844 time to fit residues: 37.2646 Evaluate side-chains 129 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5576 Z= 0.193 Angle : 0.626 11.069 7559 Z= 0.307 Chirality : 0.048 0.442 923 Planarity : 0.004 0.044 915 Dihedral : 10.208 69.357 1224 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: -1.01 (0.32), residues: 624 helix: 2.12 (0.50), residues: 106 sheet: -0.39 (0.36), residues: 177 loop : -1.81 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP X 479 HIS 0.005 0.001 HIS X 375 PHE 0.014 0.001 PHE E 78 TYR 0.017 0.002 TYR X 217 ARG 0.004 0.000 ARG E 66 *********************** 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 147 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: E 4 LEU cc_start: 0.8539 (mm) cc_final: 0.8310 (mm) REVERT: E 9 THR cc_start: 0.7554 (p) cc_final: 0.7343 (p) REVERT: E 20 LEU cc_start: 0.8250 (mt) cc_final: 0.7894 (mt) REVERT: E 47 TRP cc_start: 0.8806 (t60) cc_final: 0.7701 (t60) REVERT: F 27 GLN cc_start: 0.8670 (tm-30) cc_final: 0.7970 (tm-30) REVERT: X 102 GLU cc_start: 0.7531 (pp20) cc_final: 0.7299 (pp20) REVERT: X 410 PHE cc_start: 0.7313 (p90) cc_final: 0.6980 (p90) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1802 time to fit residues: 34.0433 Evaluate side-chains 117 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 0.0040 overall best weight: 1.1594 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5576 Z= 0.236 Angle : 0.632 7.223 7559 Z= 0.315 Chirality : 0.048 0.448 923 Planarity : 0.004 0.044 915 Dihedral : 9.595 64.676 1224 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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: 2.11 (0.51), residues: 106 sheet: -0.46 (0.36), residues: 187 loop : -1.87 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP X 479 HIS 0.005 0.001 HIS X 375 PHE 0.012 0.001 PHE E 78 TYR 0.020 0.002 TYR X 217 ARG 0.004 0.000 ARG F 77 *********************** 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 152 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: E 20 LEU cc_start: 0.8344 (mt) cc_final: 0.7940 (mt) REVERT: E 47 TRP cc_start: 0.8849 (t60) cc_final: 0.7834 (t60) REVERT: E 66 ARG cc_start: 0.8521 (ptt-90) cc_final: 0.8273 (ptt90) REVERT: F 27 GLN cc_start: 0.8687 (tm-30) cc_final: 0.7949 (tm-30) REVERT: X 280 ASN cc_start: 0.8471 (t0) cc_final: 0.8072 (t0) REVERT: X 373 MET cc_start: 0.8534 (tpp) cc_final: 0.8186 (tpp) REVERT: X 410 PHE cc_start: 0.7332 (p90) cc_final: 0.6965 (p90) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1811 time to fit residues: 35.6479 Evaluate side-chains 122 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5576 Z= 0.265 Angle : 0.668 6.381 7559 Z= 0.334 Chirality : 0.049 0.468 923 Planarity : 0.004 0.043 915 Dihedral : 9.273 60.642 1224 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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 (0.32), residues: 624 helix: 1.90 (0.50), residues: 106 sheet: -0.45 (0.36), residues: 175 loop : -1.94 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP X 479 HIS 0.004 0.001 HIS X 375 PHE 0.018 0.001 PHE E 78 TYR 0.024 0.002 TYR X 217 ARG 0.003 0.000 ARG F 42 *********************** 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 155 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: E 9 THR cc_start: 0.7837 (p) cc_final: 0.7630 (p) REVERT: E 47 TRP cc_start: 0.8898 (t60) cc_final: 0.7960 (t60) REVERT: E 66 ARG cc_start: 0.8464 (ptt-90) cc_final: 0.8228 (ptt90) REVERT: F 27 GLN cc_start: 0.8750 (tm-30) cc_final: 0.7935 (tm-30) REVERT: X 280 ASN cc_start: 0.8301 (t0) cc_final: 0.8009 (t0) REVERT: X 373 MET cc_start: 0.8616 (tpp) cc_final: 0.7975 (tpt) REVERT: X 410 PHE cc_start: 0.7251 (p90) cc_final: 0.6924 (p90) REVERT: X 457 ASP cc_start: 0.7446 (t70) cc_final: 0.7239 (t0) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1747 time to fit residues: 34.5670 Evaluate side-chains 124 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 0.0040 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 overall best weight: 0.7754 ------------------------------------------------------------------------------- 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 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5576 Z= 0.198 Angle : 0.651 7.329 7559 Z= 0.323 Chirality : 0.049 0.455 923 Planarity : 0.004 0.045 915 Dihedral : 8.781 57.042 1224 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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 : 0.00 % 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: 2.02 (0.50), residues: 106 sheet: -0.39 (0.36), residues: 177 loop : -1.90 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP X 479 HIS 0.006 0.001 HIS X 375 PHE 0.017 0.001 PHE E 78 TYR 0.024 0.002 TYR X 217 ARG 0.004 0.000 ARG F 77 *********************** 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 152 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 TRP cc_start: 0.8815 (t60) cc_final: 0.7671 (t60) REVERT: E 53 GLU cc_start: 0.8122 (pp20) cc_final: 0.7752 (pp20) REVERT: F 27 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7828 (tm-30) REVERT: X 280 ASN cc_start: 0.8348 (t0) cc_final: 0.8045 (t0) REVERT: X 373 MET cc_start: 0.8596 (tpp) cc_final: 0.7931 (tpt) REVERT: X 410 PHE cc_start: 0.7246 (p90) cc_final: 0.6913 (p90) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1647 time to fit residues: 32.5198 Evaluate side-chains 120 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2033 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= 0.213 Angle : 0.649 6.711 7559 Z= 0.323 Chirality : 0.049 0.449 923 Planarity : 0.004 0.046 915 Dihedral : 8.472 54.529 1224 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -1.20 (0.33), residues: 624 helix: 2.01 (0.51), residues: 106 sheet: -0.49 (0.37), residues: 174 loop : -1.97 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP X 479 HIS 0.004 0.001 HIS X 375 PHE 0.014 0.001 PHE E 78 TYR 0.025 0.002 TYR X 217 ARG 0.008 0.000 ARG F 77 *********************** 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 156 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: E 53 GLU cc_start: 0.8200 (pp20) cc_final: 0.7831 (pp20) REVERT: F 27 GLN cc_start: 0.8743 (tm-30) cc_final: 0.7935 (tm-30) REVERT: X 410 PHE cc_start: 0.7301 (p90) cc_final: 0.6966 (p90) REVERT: X 457 ASP cc_start: 0.7371 (t70) cc_final: 0.7167 (t0) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1809 time to fit residues: 36.0663 Evaluate side-chains 119 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5576 Z= 0.295 Angle : 0.715 8.282 7559 Z= 0.358 Chirality : 0.050 0.469 923 Planarity : 0.004 0.044 915 Dihedral : 8.639 53.794 1224 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -1.26 (0.32), residues: 624 helix: 1.86 (0.51), residues: 106 sheet: -0.46 (0.36), residues: 175 loop : -2.01 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP X 479 HIS 0.003 0.001 HIS X 287 PHE 0.018 0.002 PHE X 592 TYR 0.030 0.002 TYR X 217 ARG 0.008 0.001 ARG F 77 *********************** 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 157 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: E 47 TRP cc_start: 0.8875 (t60) cc_final: 0.7813 (t60) REVERT: E 53 GLU cc_start: 0.8304 (pp20) cc_final: 0.8020 (pp20) REVERT: F 27 GLN cc_start: 0.8788 (tm-30) cc_final: 0.7952 (tm-30) REVERT: X 102 GLU cc_start: 0.7596 (pp20) cc_final: 0.7310 (pp20) REVERT: X 114 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7985 (tm-30) REVERT: X 373 MET cc_start: 0.8945 (mmp) cc_final: 0.8690 (mmm) REVERT: X 410 PHE cc_start: 0.7179 (p90) cc_final: 0.6863 (p90) REVERT: X 457 ASP cc_start: 0.7483 (t70) cc_final: 0.7273 (t0) REVERT: X 616 ASN cc_start: 0.8698 (t0) cc_final: 0.8481 (t0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1803 time to fit residues: 36.5638 Evaluate side-chains 123 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.0020 chunk 63 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.4566 ------------------------------------------------------------------------------- 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 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5576 Z= 0.188 Angle : 0.701 8.587 7559 Z= 0.349 Chirality : 0.050 0.439 923 Planarity : 0.004 0.050 915 Dihedral : 8.121 51.601 1224 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % 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 : 0.16 % 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: -1.14 (0.33), residues: 624 helix: 2.36 (0.51), residues: 103 sheet: -0.45 (0.37), residues: 174 loop : -2.00 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP X 479 HIS 0.004 0.001 HIS X 375 PHE 0.015 0.001 PHE F 96 TYR 0.029 0.002 TYR X 217 ARG 0.007 0.001 ARG F 77 ********************** 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 158 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.9120 (tmmt) cc_final: 0.8850 (tmmt) REVERT: E 16 GLU cc_start: 0.8256 (pm20) cc_final: 0.7669 (pm20) REVERT: E 50 GLU cc_start: 0.7419 (tt0) cc_final: 0.7101 (tt0) REVERT: E 53 GLU cc_start: 0.8155 (pp20) cc_final: 0.7783 (pp20) REVERT: F 27 GLN cc_start: 0.8730 (tm-30) cc_final: 0.7923 (tm-30) REVERT: X 102 GLU cc_start: 0.7517 (pp20) cc_final: 0.7269 (pp20) REVERT: X 114 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7963 (tm-30) REVERT: X 373 MET cc_start: 0.8956 (mmp) cc_final: 0.8567 (mmt) REVERT: X 410 PHE cc_start: 0.7133 (p90) cc_final: 0.6831 (p90) REVERT: X 457 ASP cc_start: 0.7402 (t70) cc_final: 0.7200 (t0) REVERT: X 614 TRP cc_start: 0.8779 (m-10) cc_final: 0.8498 (m-90) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1682 time to fit residues: 34.2469 Evaluate side-chains 123 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 44 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.0030 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.146797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119386 restraints weight = 10182.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123008 restraints weight = 5957.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125565 restraints weight = 4258.766| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5576 Z= 0.174 Angle : 0.676 8.460 7559 Z= 0.335 Chirality : 0.049 0.427 923 Planarity : 0.004 0.051 915 Dihedral : 7.663 50.056 1224 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.18 % Allowed : 0.00 % Favored : 99.82 % 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: -1.04 (0.33), residues: 624 helix: 2.43 (0.51), residues: 103 sheet: -0.32 (0.38), residues: 172 loop : -1.96 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP X 479 HIS 0.004 0.001 HIS X 375 PHE 0.013 0.001 PHE E 78 TYR 0.026 0.002 TYR X 217 ARG 0.011 0.001 ARG F 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1577.46 seconds wall clock time: 29 minutes 8.45 seconds (1748.45 seconds total)