Starting phenix.real_space_refine on Thu Jul 24 07:44:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gp5_34190/07_2025/8gp5_34190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gp5_34190/07_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_34190/07_2025/8gp5_34190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gp5_34190/07_2025/8gp5_34190.map" model { file = "/net/cci-nas-00/data/ceres_data/8gp5_34190/07_2025/8gp5_34190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gp5_34190/07_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-5711/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: 4.08, per 1000 atoms: 0.75 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: 1.78 Conformation dependent library (CDL) restraints added in 786.9 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: 0.66 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: 1.47 Time building geometry restraints manager: 2.06 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: 0.900 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 5612 Z= 0.231 Angle : 0.849 17.193 7657 Z= 0.398 Chirality : 0.055 0.539 923 Planarity : 0.005 0.057 915 Dihedral : 16.711 114.657 2441 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 13) link_NAG-ASN : angle 3.75502 ( 39) link_ALPHA1-6 : bond 0.00308 ( 2) link_ALPHA1-6 : angle 1.56453 ( 6) link_BETA1-4 : bond 0.00523 ( 9) link_BETA1-4 : angle 1.83066 ( 27) link_ALPHA1-3 : bond 0.00685 ( 2) link_ALPHA1-3 : angle 2.61020 ( 6) hydrogen bonds : bond 0.11152 ( 168) hydrogen bonds : angle 5.77161 ( 459) SS BOND : bond 0.00369 ( 10) SS BOND : angle 1.35936 ( 20) covalent geometry : bond 0.00483 ( 5576) covalent geometry : angle 0.79526 ( 7559) *********************** 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 : 0.618 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: 0.1735 time to fit residues: 36.3525 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 : 0.579 ------------------------------------------------------------------------------- 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 5612 Z= 0.146 Angle : 0.693 15.020 7657 Z= 0.329 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 13) link_NAG-ASN : angle 3.40955 ( 39) link_ALPHA1-6 : bond 0.00774 ( 2) link_ALPHA1-6 : angle 1.69477 ( 6) link_BETA1-4 : bond 0.00469 ( 9) link_BETA1-4 : angle 1.93505 ( 27) link_ALPHA1-3 : bond 0.00550 ( 2) link_ALPHA1-3 : angle 3.00094 ( 6) hydrogen bonds : bond 0.03857 ( 168) hydrogen bonds : angle 5.14829 ( 459) SS BOND : bond 0.00432 ( 10) SS BOND : angle 0.96996 ( 20) covalent geometry : bond 0.00334 ( 5576) covalent geometry : angle 0.63292 ( 7559) *********************** 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 : 0.529 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: 0.1835 time to fit residues: 36.3974 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 : 0.579 ------------------------------------------------------------------------------- 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 5612 Z= 0.150 Angle : 0.703 14.543 7657 Z= 0.335 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 13) link_NAG-ASN : angle 3.40540 ( 39) link_ALPHA1-6 : bond 0.00350 ( 2) link_ALPHA1-6 : angle 1.65205 ( 6) link_BETA1-4 : bond 0.00443 ( 9) link_BETA1-4 : angle 1.91795 ( 27) link_ALPHA1-3 : bond 0.00688 ( 2) link_ALPHA1-3 : angle 3.11914 ( 6) hydrogen bonds : bond 0.03680 ( 168) hydrogen bonds : angle 5.02718 ( 459) SS BOND : bond 0.00475 ( 10) SS BOND : angle 1.06580 ( 20) covalent geometry : bond 0.00348 ( 5576) covalent geometry : angle 0.64446 ( 7559) *********************** 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 : 0.631 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: 0.1807 time to fit residues: 36.8198 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 : 0.617 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.146300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118650 restraints weight = 10528.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122442 restraints weight = 6082.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124766 restraints weight = 4310.285| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5612 Z= 0.130 Angle : 0.692 14.089 7657 Z= 0.326 Chirality : 0.048 0.423 923 Planarity : 0.004 0.045 915 Dihedral : 10.553 70.149 1224 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.98 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: 2.24 (0.51), residues: 106 sheet: -0.44 (0.36), residues: 177 loop : -1.85 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP X 479 HIS 0.006 0.001 HIS X 375 PHE 0.014 0.001 PHE E 78 TYR 0.012 0.002 TYR X 40 ARG 0.004 0.001 ARG E 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 13) link_NAG-ASN : angle 3.30319 ( 39) link_ALPHA1-6 : bond 0.00511 ( 2) link_ALPHA1-6 : angle 1.85215 ( 6) link_BETA1-4 : bond 0.00405 ( 9) link_BETA1-4 : angle 1.95252 ( 27) link_ALPHA1-3 : bond 0.00627 ( 2) link_ALPHA1-3 : angle 3.18059 ( 6) hydrogen bonds : bond 0.03406 ( 168) hydrogen bonds : angle 4.90131 ( 459) SS BOND : bond 0.00446 ( 10) SS BOND : angle 0.93514 ( 20) covalent geometry : bond 0.00298 ( 5576) covalent geometry : angle 0.63385 ( 7559) *********************** 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 : 0.580 Fit side-chains revert: symmetry clash REVERT: E 20 LEU cc_start: 0.8270 (mt) cc_final: 0.7913 (mt) REVERT: E 47 TRP cc_start: 0.8715 (t60) cc_final: 0.7541 (t60) REVERT: F 27 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7633 (tm-30) REVERT: X 102 GLU cc_start: 0.7439 (pp20) cc_final: 0.7195 (pp20) REVERT: X 280 ASN cc_start: 0.8193 (t0) cc_final: 0.7916 (t0) REVERT: X 410 PHE cc_start: 0.7281 (p90) cc_final: 0.6960 (p90) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1734 time to fit residues: 34.4027 Evaluate side-chains 130 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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: 0.4980 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.145245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117585 restraints weight = 10403.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121273 restraints weight = 6080.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123765 restraints weight = 4338.692| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5612 Z= 0.134 Angle : 0.690 13.831 7657 Z= 0.326 Chirality : 0.048 0.421 923 Planarity : 0.004 0.044 915 Dihedral : 9.298 64.700 1224 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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: -1.07 (0.33), residues: 624 helix: 2.25 (0.50), residues: 106 sheet: -0.51 (0.37), residues: 174 loop : -1.86 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP X 479 HIS 0.005 0.001 HIS X 375 PHE 0.012 0.001 PHE E 78 TYR 0.014 0.002 TYR X 217 ARG 0.004 0.001 ARG F 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 13) link_NAG-ASN : angle 3.25520 ( 39) link_ALPHA1-6 : bond 0.00427 ( 2) link_ALPHA1-6 : angle 1.89836 ( 6) link_BETA1-4 : bond 0.00422 ( 9) link_BETA1-4 : angle 2.09055 ( 27) link_ALPHA1-3 : bond 0.00501 ( 2) link_ALPHA1-3 : angle 3.17386 ( 6) hydrogen bonds : bond 0.03377 ( 168) hydrogen bonds : angle 4.84995 ( 459) SS BOND : bond 0.00744 ( 10) SS BOND : angle 1.12801 ( 20) covalent geometry : bond 0.00308 ( 5576) covalent geometry : angle 0.63019 ( 7559) *********************** 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 156 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: E 9 THR cc_start: 0.7434 (p) cc_final: 0.7198 (p) REVERT: E 20 LEU cc_start: 0.8278 (mt) cc_final: 0.7878 (mt) REVERT: E 47 TRP cc_start: 0.8730 (t60) cc_final: 0.7571 (t60) REVERT: F 27 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7796 (tm-30) REVERT: X 280 ASN cc_start: 0.8592 (t0) cc_final: 0.8282 (t0) REVERT: X 373 MET cc_start: 0.8321 (tpp) cc_final: 0.8003 (tpp) REVERT: X 410 PHE cc_start: 0.7287 (p90) cc_final: 0.6937 (p90) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1735 time to fit residues: 35.1951 Evaluate side-chains 122 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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: 0.0970 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.142677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116229 restraints weight = 10050.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119971 restraints weight = 5522.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.122608 restraints weight = 3792.088| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5612 Z= 0.132 Angle : 0.675 13.563 7657 Z= 0.325 Chirality : 0.048 0.425 923 Planarity : 0.004 0.043 915 Dihedral : 8.775 59.907 1224 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.18 % Allowed : 2.80 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.20 (0.51), residues: 106 sheet: -0.54 (0.37), residues: 174 loop : -1.87 (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 0.019 0.001 PHE E 78 TYR 0.015 0.001 TYR E 91 ARG 0.003 0.001 ARG F 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 13) link_NAG-ASN : angle 3.17426 ( 39) link_ALPHA1-6 : bond 0.00431 ( 2) link_ALPHA1-6 : angle 1.86593 ( 6) link_BETA1-4 : bond 0.00433 ( 9) link_BETA1-4 : angle 1.53585 ( 27) link_ALPHA1-3 : bond 0.00553 ( 2) link_ALPHA1-3 : angle 3.34002 ( 6) hydrogen bonds : bond 0.03315 ( 168) hydrogen bonds : angle 4.84456 ( 459) SS BOND : bond 0.00492 ( 10) SS BOND : angle 1.16699 ( 20) covalent geometry : bond 0.00305 ( 5576) covalent geometry : angle 0.62153 ( 7559) *********************** 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: 1 poor density : 153 time to evaluate : 0.563 Fit side-chains REVERT: E 9 THR cc_start: 0.7505 (p) cc_final: 0.7303 (p) REVERT: E 20 LEU cc_start: 0.8428 (mt) cc_final: 0.8080 (mt) REVERT: E 47 TRP cc_start: 0.8792 (t60) cc_final: 0.7658 (t60) REVERT: F 27 GLN cc_start: 0.8534 (tm-30) cc_final: 0.7905 (tm-30) REVERT: X 102 GLU cc_start: 0.7264 (pp20) cc_final: 0.7015 (pp20) REVERT: X 280 ASN cc_start: 0.8544 (t0) cc_final: 0.8190 (t0) REVERT: X 410 PHE cc_start: 0.7339 (p90) cc_final: 0.7023 (p90) REVERT: X 457 ASP cc_start: 0.7381 (t70) cc_final: 0.7174 (t0) outliers start: 1 outliers final: 1 residues processed: 153 average time/residue: 0.1567 time to fit residues: 31.6351 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 : 0.582 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.143745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115593 restraints weight = 10393.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119255 restraints weight = 6196.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121632 restraints weight = 4459.055| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5612 Z= 0.165 Angle : 0.713 13.706 7657 Z= 0.342 Chirality : 0.049 0.435 923 Planarity : 0.004 0.045 915 Dihedral : 8.549 56.713 1224 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: -1.14 (0.33), residues: 624 helix: 2.16 (0.51), residues: 106 sheet: -0.60 (0.37), residues: 174 loop : -1.87 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP X 479 HIS 0.005 0.001 HIS X 375 PHE 0.017 0.001 PHE E 78 TYR 0.014 0.002 TYR X 40 ARG 0.004 0.001 ARG F 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 13) link_NAG-ASN : angle 3.20813 ( 39) link_ALPHA1-6 : bond 0.00432 ( 2) link_ALPHA1-6 : angle 1.90692 ( 6) link_BETA1-4 : bond 0.00346 ( 9) link_BETA1-4 : angle 1.65552 ( 27) link_ALPHA1-3 : bond 0.00565 ( 2) link_ALPHA1-3 : angle 3.21133 ( 6) hydrogen bonds : bond 0.03579 ( 168) hydrogen bonds : angle 4.85850 ( 459) SS BOND : bond 0.00527 ( 10) SS BOND : angle 1.20544 ( 20) covalent geometry : bond 0.00384 ( 5576) covalent geometry : angle 0.66157 ( 7559) *********************** 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 to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.609 Fit side-chains REVERT: E 20 LEU cc_start: 0.8446 (mt) cc_final: 0.8107 (mt) REVERT: E 47 TRP cc_start: 0.8752 (t60) cc_final: 0.7670 (t60) REVERT: F 27 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7839 (tm-30) REVERT: X 102 GLU cc_start: 0.7319 (pp20) cc_final: 0.7020 (pp20) REVERT: X 280 ASN cc_start: 0.8511 (t0) cc_final: 0.8140 (t0) REVERT: X 410 PHE cc_start: 0.7240 (p90) cc_final: 0.6934 (p90) REVERT: X 457 ASP cc_start: 0.7396 (t70) cc_final: 0.7185 (t0) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1853 time to fit residues: 36.6064 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 : 0.629 ------------------------------------------------------------------------------- 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: 0.1980 chunk 20 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 53 optimal weight: 6.9990 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 = 0.3779 r_free = 0.3779 target = 0.144000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116080 restraints weight = 10331.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119665 restraints weight = 6135.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122106 restraints weight = 4401.998| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5612 Z= 0.154 Angle : 0.727 13.712 7657 Z= 0.352 Chirality : 0.049 0.447 923 Planarity : 0.004 0.044 915 Dihedral : 8.274 54.699 1224 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.17 (0.51), residues: 106 sheet: -0.64 (0.37), residues: 184 loop : -1.87 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP X 479 HIS 0.004 0.001 HIS X 375 PHE 0.015 0.001 PHE E 78 TYR 0.024 0.002 TYR X 217 ARG 0.006 0.001 ARG X 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 13) link_NAG-ASN : angle 3.18925 ( 39) link_ALPHA1-6 : bond 0.00490 ( 2) link_ALPHA1-6 : angle 1.93070 ( 6) link_BETA1-4 : bond 0.00359 ( 9) link_BETA1-4 : angle 1.58629 ( 27) link_ALPHA1-3 : bond 0.00553 ( 2) link_ALPHA1-3 : angle 3.26196 ( 6) hydrogen bonds : bond 0.03515 ( 168) hydrogen bonds : angle 4.86286 ( 459) SS BOND : bond 0.00483 ( 10) SS BOND : angle 1.26134 ( 20) covalent geometry : bond 0.00358 ( 5576) covalent geometry : angle 0.67737 ( 7559) *********************** 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 153 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: E 47 TRP cc_start: 0.8741 (t60) cc_final: 0.7679 (t60) REVERT: E 53 GLU cc_start: 0.8635 (pm20) cc_final: 0.8406 (pp20) REVERT: F 27 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7862 (tm-30) REVERT: X 102 GLU cc_start: 0.7229 (pp20) cc_final: 0.6996 (pp20) REVERT: X 280 ASN cc_start: 0.8355 (t0) cc_final: 0.8073 (t0) REVERT: X 410 PHE cc_start: 0.7262 (p90) cc_final: 0.6959 (p90) REVERT: X 457 ASP cc_start: 0.7438 (t70) cc_final: 0.7234 (t0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1667 time to fit residues: 33.2638 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 : 0.628 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.141914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113370 restraints weight = 10335.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117031 restraints weight = 6196.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119487 restraints weight = 4466.982| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5612 Z= 0.189 Angle : 0.775 13.638 7657 Z= 0.372 Chirality : 0.051 0.444 923 Planarity : 0.004 0.041 915 Dihedral : 8.384 54.039 1224 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % 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: 2.11 (0.51), residues: 106 sheet: -0.70 (0.37), residues: 182 loop : -1.86 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP X 479 HIS 0.006 0.002 HIS X 375 PHE 0.015 0.001 PHE E 78 TYR 0.017 0.002 TYR X 638 ARG 0.005 0.001 ARG X 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 13) link_NAG-ASN : angle 3.28537 ( 39) link_ALPHA1-6 : bond 0.00393 ( 2) link_ALPHA1-6 : angle 1.89269 ( 6) link_BETA1-4 : bond 0.00327 ( 9) link_BETA1-4 : angle 1.61013 ( 27) link_ALPHA1-3 : bond 0.00564 ( 2) link_ALPHA1-3 : angle 3.25226 ( 6) hydrogen bonds : bond 0.03774 ( 168) hydrogen bonds : angle 4.93066 ( 459) SS BOND : bond 0.00523 ( 10) SS BOND : angle 1.64163 ( 20) covalent geometry : bond 0.00440 ( 5576) covalent geometry : angle 0.72412 ( 7559) *********************** 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 : 0.622 Fit side-chains revert: symmetry clash REVERT: E 9 THR cc_start: 0.7862 (p) cc_final: 0.7656 (p) REVERT: E 47 TRP cc_start: 0.8773 (t60) cc_final: 0.7719 (t60) REVERT: E 87 MET cc_start: 0.8210 (tpp) cc_final: 0.7728 (tpp) REVERT: F 27 GLN cc_start: 0.8562 (tm-30) cc_final: 0.7792 (tm-30) REVERT: X 102 GLU cc_start: 0.7321 (pp20) cc_final: 0.7035 (pp20) REVERT: X 280 ASN cc_start: 0.8259 (t0) cc_final: 0.8034 (t0) REVERT: X 373 MET cc_start: 0.8874 (mmp) cc_final: 0.8593 (mmm) REVERT: X 410 PHE cc_start: 0.7086 (p90) cc_final: 0.6829 (p90) REVERT: X 457 ASP cc_start: 0.7449 (t70) cc_final: 0.7220 (t0) REVERT: X 626 MET cc_start: 0.7031 (ttm) cc_final: 0.6310 (ttp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1949 time to fit residues: 37.5702 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 : 0.645 ------------------------------------------------------------------------------- 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: 0.8980 chunk 63 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 60 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.144870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117062 restraints weight = 10374.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120761 restraints weight = 6100.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123200 restraints weight = 4339.903| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5612 Z= 0.144 Angle : 0.755 13.489 7657 Z= 0.363 Chirality : 0.050 0.443 923 Planarity : 0.004 0.045 915 Dihedral : 8.174 52.597 1224 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.09 (0.33), residues: 624 helix: 2.47 (0.52), residues: 103 sheet: -0.59 (0.37), residues: 184 loop : -1.91 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP X 479 HIS 0.006 0.001 HIS X 375 PHE 0.014 0.001 PHE X 592 TYR 0.018 0.002 TYR X 40 ARG 0.005 0.001 ARG F 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 13) link_NAG-ASN : angle 3.14186 ( 39) link_ALPHA1-6 : bond 0.00522 ( 2) link_ALPHA1-6 : angle 1.93853 ( 6) link_BETA1-4 : bond 0.00368 ( 9) link_BETA1-4 : angle 1.55922 ( 27) link_ALPHA1-3 : bond 0.00602 ( 2) link_ALPHA1-3 : angle 3.26765 ( 6) hydrogen bonds : bond 0.03540 ( 168) hydrogen bonds : angle 4.93884 ( 459) SS BOND : bond 0.00435 ( 10) SS BOND : angle 1.34036 ( 20) covalent geometry : bond 0.00334 ( 5576) covalent geometry : angle 0.70798 ( 7559) ********************** 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 157 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 9 THR cc_start: 0.7735 (p) cc_final: 0.7497 (p) REVERT: E 47 TRP cc_start: 0.8732 (t60) cc_final: 0.7682 (t60) REVERT: E 86 ASP cc_start: 0.7769 (p0) cc_final: 0.7403 (p0) REVERT: E 87 MET cc_start: 0.8134 (tpp) cc_final: 0.7610 (tpp) REVERT: F 27 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7761 (tm-30) REVERT: X 40 TYR cc_start: 0.8405 (t80) cc_final: 0.8177 (t80) REVERT: X 102 GLU cc_start: 0.7286 (pp20) cc_final: 0.7050 (pp20) REVERT: X 280 ASN cc_start: 0.8379 (t0) cc_final: 0.8145 (t0) REVERT: X 410 PHE cc_start: 0.7108 (p90) cc_final: 0.6831 (p90) REVERT: X 457 ASP cc_start: 0.7439 (t70) cc_final: 0.7237 (t0) REVERT: X 614 TRP cc_start: 0.8829 (m-10) cc_final: 0.8489 (m-90) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1744 time to fit residues: 35.6683 Evaluate side-chains 121 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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: 0.0020 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 45 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119002 restraints weight = 10326.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122754 restraints weight = 5982.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125354 restraints weight = 4215.358| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 5612 Z= 0.135 Angle : 0.747 13.319 7657 Z= 0.360 Chirality : 0.050 0.435 923 Planarity : 0.004 0.042 915 Dihedral : 7.889 51.334 1224 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.18 % Allowed : 0.88 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.51 (0.52), residues: 103 sheet: -0.54 (0.37), residues: 184 loop : -1.91 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP X 479 HIS 0.005 0.001 HIS X 375 PHE 0.013 0.001 PHE E 78 TYR 0.017 0.002 TYR X 40 ARG 0.005 0.001 ARG E 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 13) link_NAG-ASN : angle 3.05264 ( 39) link_ALPHA1-6 : bond 0.00548 ( 2) link_ALPHA1-6 : angle 1.95202 ( 6) link_BETA1-4 : bond 0.00380 ( 9) link_BETA1-4 : angle 1.54175 ( 27) link_ALPHA1-3 : bond 0.00641 ( 2) link_ALPHA1-3 : angle 3.26631 ( 6) hydrogen bonds : bond 0.03357 ( 168) hydrogen bonds : angle 4.87343 ( 459) SS BOND : bond 0.00383 ( 10) SS BOND : angle 1.25356 ( 20) covalent geometry : bond 0.00316 ( 5576) covalent geometry : angle 0.70218 ( 7559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2107.54 seconds wall clock time: 37 minutes 31.16 seconds (2251.16 seconds total)