Starting phenix.real_space_refine on Fri Mar 15 12:07:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcb_21605/03_2024/6wcb_21605.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcb_21605/03_2024/6wcb_21605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcb_21605/03_2024/6wcb_21605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcb_21605/03_2024/6wcb_21605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcb_21605/03_2024/6wcb_21605.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcb_21605/03_2024/6wcb_21605.pdb" } resolution = 3.17 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cs 7 16.47 5 S 38 5.16 5 C 3754 2.51 5 N 938 2.21 5 O 1006 1.98 5 H 5904 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 63": "OE1" <-> "OE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B ASP 283": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11647 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5800 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5800 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CS': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 5.92, per 1000 atoms: 0.51 Number of scatterers: 11647 At special positions: 0 Unit cell: (105.536, 72.896, 77.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cs 7 54.66 S 38 16.00 O 1006 8.00 N 938 7.00 C 3754 6.00 H 5904 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.35 Conformation dependent library (CDL) restraints added in 1.3 seconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 66 through 102 Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 137 through 164 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 257 through 284 removed outlier: 5.074A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.642A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 332 Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 368 through 400 removed outlier: 3.798A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.585A pdb=" N TRP A 410 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 439 removed outlier: 5.239A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 507 Processing helix chain 'B' and resid 33 through 49 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 66 through 102 Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 137 through 164 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 257 through 284 removed outlier: 5.074A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.643A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 331 Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 368 through 400 removed outlier: 3.797A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 373 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.583A pdb=" N TRP B 410 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 439 removed outlier: 5.238A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 475 465 hydrogen bonds defined for protein. 1383 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: 4.50 Time building geometry restraints manager: 11.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5886 1.03 - 1.23: 18 1.23 - 1.42: 2380 1.42 - 1.61: 3392 1.61 - 1.81: 58 Bond restraints: 11734 Sorted by residual: bond pdb=" C THR B 472 " pdb=" N LEU B 473 " ideal model delta sigma weight residual 1.335 1.550 -0.215 1.38e-02 5.25e+03 2.43e+02 bond pdb=" C THR A 472 " pdb=" N LEU A 505 " ideal model delta sigma weight residual 1.335 1.550 -0.215 1.38e-02 5.25e+03 2.43e+02 bond pdb=" C THR B 306 " pdb=" N GLY B 307 " ideal model delta sigma weight residual 1.340 1.330 0.010 6.60e-03 2.30e+04 2.49e+00 bond pdb=" C THR A 306 " pdb=" N GLY A 307 " ideal model delta sigma weight residual 1.340 1.330 0.010 6.60e-03 2.30e+04 2.40e+00 bond pdb=" CA GLY B 307 " pdb=" C GLY B 307 " ideal model delta sigma weight residual 1.511 1.517 -0.006 6.90e-03 2.10e+04 7.80e-01 ... (remaining 11729 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.16: 250 107.16 - 113.88: 14087 113.88 - 120.59: 4167 120.59 - 127.30: 2696 127.30 - 134.02: 68 Bond angle restraints: 21268 Sorted by residual: angle pdb=" CA GLY A 307 " pdb=" C GLY A 307 " pdb=" N PRO A 308 " ideal model delta sigma weight residual 119.27 117.28 1.99 8.50e-01 1.38e+00 5.49e+00 angle pdb=" CA GLY B 307 " pdb=" C GLY B 307 " pdb=" N PRO B 308 " ideal model delta sigma weight residual 119.27 117.30 1.97 8.50e-01 1.38e+00 5.37e+00 angle pdb=" CA GLY A 307 " pdb=" C GLY A 307 " pdb=" O GLY A 307 " ideal model delta sigma weight residual 119.65 121.03 -1.38 6.70e-01 2.23e+00 4.27e+00 angle pdb=" CA GLY B 307 " pdb=" C GLY B 307 " pdb=" O GLY B 307 " ideal model delta sigma weight residual 119.65 121.01 -1.36 6.70e-01 2.23e+00 4.11e+00 angle pdb=" N ARG B 442 " pdb=" CA ARG B 442 " pdb=" C ARG B 442 " ideal model delta sigma weight residual 113.18 110.75 2.43 1.33e+00 5.65e-01 3.33e+00 ... (remaining 21263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 4937 14.97 - 29.94: 399 29.94 - 44.92: 97 44.92 - 59.89: 89 59.89 - 74.86: 6 Dihedral angle restraints: 5528 sinusoidal: 2936 harmonic: 2592 Sorted by residual: dihedral pdb=" CA PHE B 99 " pdb=" C PHE B 99 " pdb=" N GLN B 100 " pdb=" CA GLN B 100 " ideal model delta harmonic sigma weight residual 180.00 164.56 15.44 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CA PHE A 99 " pdb=" C PHE A 99 " pdb=" N GLN A 100 " pdb=" CA GLN A 100 " ideal model delta harmonic sigma weight residual 180.00 164.62 15.38 0 5.00e+00 4.00e-02 9.47e+00 dihedral pdb=" CB MET B 51 " pdb=" CG MET B 51 " pdb=" SD MET B 51 " pdb=" CE MET B 51 " ideal model delta sinusoidal sigma weight residual 180.00 123.83 56.17 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 666 0.024 - 0.047: 159 0.047 - 0.071: 91 0.071 - 0.095: 48 0.095 - 0.119: 14 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA VAL B 285 " pdb=" N VAL B 285 " pdb=" C VAL B 285 " pdb=" CB VAL B 285 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA VAL A 102 " pdb=" N VAL A 102 " pdb=" C VAL A 102 " pdb=" CB VAL A 102 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA VAL A 285 " pdb=" N VAL A 285 " pdb=" C VAL A 285 " pdb=" CB VAL A 285 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 975 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 420 " -0.005 2.00e-02 2.50e+03 9.58e-03 2.75e+00 pdb=" CG PHE A 420 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 420 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 420 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 420 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 420 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 420 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 420 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 420 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 420 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 420 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 420 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 420 " -0.010 2.00e-02 2.50e+03 9.16e-03 2.52e+00 pdb=" CG PHE B 420 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 420 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 420 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 420 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 420 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 420 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE B 420 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE B 420 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE B 420 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE B 420 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 420 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 307 " -0.015 5.00e-02 4.00e+02 2.19e-02 7.71e-01 pdb=" N PRO B 308 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO B 308 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 308 " -0.012 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.45: 6508 2.45 - 3.30: 44661 3.30 - 4.15: 61665 4.15 - 5.01: 110976 5.01 - 5.86: 148706 Nonbonded interactions: 372516 Sorted by model distance: nonbonded pdb=" HH TYR A 359 " pdb=" OE1 GLN A 452 " model vdw 1.596 1.850 nonbonded pdb=" HH TYR B 359 " pdb=" OE1 GLN B 452 " model vdw 1.597 1.850 nonbonded pdb=" HG1 THR A 319 " pdb=" OH TYR A 359 " model vdw 1.606 1.850 nonbonded pdb=" HE2 HIS B 95 " pdb=" OD1 ASN B 113 " model vdw 1.617 1.850 nonbonded pdb=" HE2 HIS A 95 " pdb=" OD1 ASN A 113 " model vdw 1.617 1.850 ... (remaining 372511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 508 or resid 701 through 703)) selection = chain 'B' } 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 individual isotropic 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: 0.030 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: 0.170 Extract box with map and model: 0.880 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 48.690 Find NCS groups from input model: 0.500 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: 0.010 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: 53.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 0.215 5830 Z= 0.321 Angle : 0.414 4.336 7946 Z= 0.240 Chirality : 0.033 0.119 978 Planarity : 0.003 0.022 974 Dihedral : 13.865 74.862 2034 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.29 % Allowed : 6.80 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.30), residues: 726 helix: 1.01 (0.21), residues: 595 sheet: None (None), residues: 0 loop : -2.39 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 394 HIS 0.003 0.001 HIS A 328 PHE 0.025 0.001 PHE A 420 TYR 0.004 0.001 TYR B 313 ARG 0.001 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7772 (tt0) cc_final: 0.7483 (tt0) REVERT: A 339 ARG cc_start: 0.6755 (tpt170) cc_final: 0.5835 (ttm-80) REVERT: A 451 MET cc_start: 0.7484 (mmt) cc_final: 0.7222 (ttt) REVERT: B 34 GLN cc_start: 0.7839 (tt0) cc_final: 0.7521 (tt0) REVERT: B 339 ARG cc_start: 0.6756 (tpt170) cc_final: 0.5742 (ttm-80) REVERT: B 451 MET cc_start: 0.7501 (mmt) cc_final: 0.7168 (ttt) outliers start: 8 outliers final: 4 residues processed: 139 average time/residue: 0.3762 time to fit residues: 69.6446 Evaluate side-chains 115 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5830 Z= 0.298 Angle : 0.522 5.057 7946 Z= 0.275 Chirality : 0.037 0.131 978 Planarity : 0.004 0.037 974 Dihedral : 5.156 56.034 784 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.27 % Allowed : 10.36 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.32), residues: 726 helix: 1.85 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.89 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 324 HIS 0.008 0.001 HIS A 328 PHE 0.013 0.002 PHE A 389 TYR 0.009 0.002 TYR A 160 ARG 0.002 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7830 (tt0) cc_final: 0.7454 (tt0) REVERT: A 131 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8095 (t) REVERT: A 339 ARG cc_start: 0.6867 (tpt170) cc_final: 0.6101 (mtp85) REVERT: A 451 MET cc_start: 0.7585 (mmt) cc_final: 0.7243 (ttt) REVERT: B 34 GLN cc_start: 0.7912 (tt0) cc_final: 0.7585 (tt0) REVERT: B 131 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8026 (t) REVERT: B 339 ARG cc_start: 0.6813 (tpt170) cc_final: 0.6117 (mtp85) REVERT: B 451 MET cc_start: 0.7548 (mmt) cc_final: 0.7263 (ttt) outliers start: 14 outliers final: 10 residues processed: 139 average time/residue: 0.4698 time to fit residues: 82.8832 Evaluate side-chains 140 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 472 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5830 Z= 0.251 Angle : 0.466 4.316 7946 Z= 0.249 Chirality : 0.036 0.139 978 Planarity : 0.004 0.023 974 Dihedral : 5.063 52.187 784 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.94 % Allowed : 12.14 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.32), residues: 726 helix: 2.14 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.22 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 394 HIS 0.005 0.001 HIS A 328 PHE 0.009 0.001 PHE A 351 TYR 0.006 0.001 TYR A 359 ARG 0.005 0.001 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7864 (tt0) cc_final: 0.7452 (tt0) REVERT: A 131 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8166 (t) REVERT: A 339 ARG cc_start: 0.6934 (tpt170) cc_final: 0.6133 (mtp85) REVERT: A 451 MET cc_start: 0.7583 (mmt) cc_final: 0.7246 (ttt) REVERT: B 34 GLN cc_start: 0.7960 (tt0) cc_final: 0.7613 (tt0) REVERT: B 131 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8165 (t) REVERT: B 339 ARG cc_start: 0.6864 (tpt170) cc_final: 0.6162 (mtp85) REVERT: B 451 MET cc_start: 0.7568 (mmt) cc_final: 0.7254 (ttt) outliers start: 12 outliers final: 4 residues processed: 139 average time/residue: 0.4428 time to fit residues: 77.9407 Evaluate side-chains 139 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5830 Z= 0.262 Angle : 0.482 4.322 7946 Z= 0.257 Chirality : 0.037 0.169 978 Planarity : 0.004 0.024 974 Dihedral : 4.968 49.709 784 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.29 % Allowed : 12.78 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.32), residues: 726 helix: 2.25 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -0.87 (0.62), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 324 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE B 389 TYR 0.008 0.001 TYR A 359 ARG 0.005 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7874 (tt0) cc_final: 0.7457 (tt0) REVERT: A 131 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8249 (t) REVERT: A 339 ARG cc_start: 0.6951 (tpt170) cc_final: 0.6119 (mtp85) REVERT: A 451 MET cc_start: 0.7642 (mmt) cc_final: 0.7330 (ttt) REVERT: B 34 GLN cc_start: 0.7936 (tt0) cc_final: 0.7609 (tt0) REVERT: B 131 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8367 (t) REVERT: B 339 ARG cc_start: 0.6872 (tpt170) cc_final: 0.6131 (mtp85) REVERT: B 451 MET cc_start: 0.7610 (mmt) cc_final: 0.7318 (ttt) outliers start: 8 outliers final: 4 residues processed: 142 average time/residue: 0.4576 time to fit residues: 82.0246 Evaluate side-chains 140 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5830 Z= 0.265 Angle : 0.470 4.362 7946 Z= 0.251 Chirality : 0.036 0.134 978 Planarity : 0.003 0.025 974 Dihedral : 4.809 48.676 784 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.94 % Allowed : 12.46 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.32), residues: 726 helix: 2.26 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -0.77 (0.61), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 394 HIS 0.006 0.001 HIS A 328 PHE 0.010 0.001 PHE B 389 TYR 0.007 0.001 TYR A 359 ARG 0.005 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7912 (tt0) cc_final: 0.7503 (tt0) REVERT: A 339 ARG cc_start: 0.6992 (tpt170) cc_final: 0.6110 (mtp85) REVERT: A 451 MET cc_start: 0.7603 (mmt) cc_final: 0.7297 (ttt) REVERT: B 34 GLN cc_start: 0.7945 (tt0) cc_final: 0.7643 (tt0) REVERT: B 156 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7698 (tt) REVERT: B 339 ARG cc_start: 0.6879 (tpt170) cc_final: 0.5835 (ttm-80) REVERT: B 451 MET cc_start: 0.7600 (mmt) cc_final: 0.7304 (ttt) outliers start: 12 outliers final: 6 residues processed: 149 average time/residue: 0.4324 time to fit residues: 83.2803 Evaluate side-chains 145 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5830 Z= 0.354 Angle : 0.509 4.415 7946 Z= 0.274 Chirality : 0.038 0.189 978 Planarity : 0.004 0.028 974 Dihedral : 4.174 36.809 782 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.46 % Allowed : 13.92 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.32), residues: 726 helix: 2.16 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -0.79 (0.61), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.012 0.002 PHE B 389 TYR 0.008 0.002 TYR A 359 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7933 (tt0) cc_final: 0.7547 (tt0) REVERT: A 339 ARG cc_start: 0.7000 (tpt170) cc_final: 0.5841 (ttm-80) REVERT: A 451 MET cc_start: 0.7672 (mmt) cc_final: 0.7343 (ttt) REVERT: B 34 GLN cc_start: 0.7966 (tt0) cc_final: 0.7662 (tt0) REVERT: B 156 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7707 (tt) REVERT: B 339 ARG cc_start: 0.6945 (tpt170) cc_final: 0.5869 (ttm-80) REVERT: B 451 MET cc_start: 0.7672 (mmt) cc_final: 0.7349 (ttt) REVERT: B 463 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8314 (mtt90) outliers start: 9 outliers final: 6 residues processed: 144 average time/residue: 0.4336 time to fit residues: 80.1465 Evaluate side-chains 147 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5830 Z= 0.171 Angle : 0.450 4.165 7946 Z= 0.238 Chirality : 0.035 0.131 978 Planarity : 0.003 0.028 974 Dihedral : 3.896 28.298 782 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.65 % Allowed : 15.70 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.32), residues: 726 helix: 2.48 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.71 (0.63), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 394 HIS 0.005 0.001 HIS A 328 PHE 0.008 0.001 PHE B 99 TYR 0.007 0.001 TYR A 359 ARG 0.003 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7908 (tt0) cc_final: 0.7496 (tt0) REVERT: A 309 ARG cc_start: 0.7146 (mtt-85) cc_final: 0.6878 (mmm-85) REVERT: A 339 ARG cc_start: 0.6991 (tpt170) cc_final: 0.5844 (ttm-80) REVERT: A 451 MET cc_start: 0.7648 (mmt) cc_final: 0.7298 (ttt) REVERT: B 34 GLN cc_start: 0.7913 (tt0) cc_final: 0.7611 (tt0) REVERT: B 156 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7721 (tt) REVERT: B 309 ARG cc_start: 0.7198 (mtt-85) cc_final: 0.6871 (mmm-85) REVERT: B 339 ARG cc_start: 0.6921 (tpt170) cc_final: 0.5840 (ttm-80) REVERT: B 451 MET cc_start: 0.7612 (mmt) cc_final: 0.7300 (ttt) REVERT: B 463 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8270 (mtt90) outliers start: 4 outliers final: 2 residues processed: 145 average time/residue: 0.4669 time to fit residues: 85.5049 Evaluate side-chains 147 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 259 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5830 Z= 0.241 Angle : 0.469 4.277 7946 Z= 0.249 Chirality : 0.036 0.131 978 Planarity : 0.003 0.028 974 Dihedral : 3.670 20.647 780 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.97 % Allowed : 15.53 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.32), residues: 726 helix: 2.43 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.68 (0.63), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 394 HIS 0.006 0.001 HIS A 328 PHE 0.011 0.001 PHE A 389 TYR 0.008 0.001 TYR A 359 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7900 (tt0) cc_final: 0.7503 (tt0) REVERT: A 309 ARG cc_start: 0.7163 (mtt-85) cc_final: 0.6894 (mmm-85) REVERT: A 339 ARG cc_start: 0.7011 (tpt170) cc_final: 0.5870 (ttm-80) REVERT: A 451 MET cc_start: 0.7654 (mmt) cc_final: 0.7308 (ttt) REVERT: B 34 GLN cc_start: 0.7947 (tt0) cc_final: 0.7655 (tt0) REVERT: B 156 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7729 (tt) REVERT: B 309 ARG cc_start: 0.7158 (mtt-85) cc_final: 0.6847 (mmm-85) REVERT: B 339 ARG cc_start: 0.6934 (tpt170) cc_final: 0.5847 (ttm-80) REVERT: B 451 MET cc_start: 0.7623 (mmt) cc_final: 0.7312 (ttt) REVERT: B 463 ARG cc_start: 0.8542 (mtp85) cc_final: 0.8322 (mtt90) outliers start: 6 outliers final: 5 residues processed: 148 average time/residue: 0.4656 time to fit residues: 87.1943 Evaluate side-chains 151 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 284 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5830 Z= 0.212 Angle : 0.465 4.232 7946 Z= 0.247 Chirality : 0.036 0.146 978 Planarity : 0.003 0.029 974 Dihedral : 3.707 26.917 780 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.13 % Allowed : 15.37 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.32), residues: 726 helix: 2.48 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.60 (0.63), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 394 HIS 0.006 0.001 HIS A 328 PHE 0.010 0.001 PHE B 389 TYR 0.007 0.001 TYR A 359 ARG 0.002 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7899 (tt0) cc_final: 0.7502 (tt0) REVERT: A 309 ARG cc_start: 0.7158 (mtt-85) cc_final: 0.6888 (mmm-85) REVERT: A 339 ARG cc_start: 0.7010 (tpt170) cc_final: 0.5871 (ttm-80) REVERT: A 451 MET cc_start: 0.7636 (mmt) cc_final: 0.7278 (ttt) REVERT: B 34 GLN cc_start: 0.7914 (tt0) cc_final: 0.7619 (tt0) REVERT: B 156 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7734 (tt) REVERT: B 309 ARG cc_start: 0.7175 (mtt-85) cc_final: 0.6867 (mmm-85) REVERT: B 339 ARG cc_start: 0.6941 (tpt170) cc_final: 0.5864 (ttm-80) REVERT: B 451 MET cc_start: 0.7616 (mmt) cc_final: 0.7310 (ttt) REVERT: B 463 ARG cc_start: 0.8538 (mtp85) cc_final: 0.8323 (mtt90) outliers start: 7 outliers final: 6 residues processed: 149 average time/residue: 0.4587 time to fit residues: 86.1549 Evaluate side-chains 153 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 66 optimal weight: 0.3980 chunk 57 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5830 Z= 0.132 Angle : 0.434 4.111 7946 Z= 0.227 Chirality : 0.035 0.126 978 Planarity : 0.003 0.030 974 Dihedral : 3.553 22.310 780 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.49 % Allowed : 16.18 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.32), residues: 726 helix: 2.66 (0.21), residues: 605 sheet: None (None), residues: 0 loop : -0.40 (0.64), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.007 0.001 PHE A 99 TYR 0.006 0.001 TYR A 359 ARG 0.001 0.000 ARG B 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7839 (tt0) cc_final: 0.7465 (tt0) REVERT: A 309 ARG cc_start: 0.7118 (mtt-85) cc_final: 0.6807 (mmm-85) REVERT: A 339 ARG cc_start: 0.7021 (tpt170) cc_final: 0.6178 (mtp85) REVERT: A 451 MET cc_start: 0.7618 (mmt) cc_final: 0.7271 (ttt) REVERT: B 34 GLN cc_start: 0.7915 (tt0) cc_final: 0.7602 (tt0) REVERT: B 156 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7746 (tt) REVERT: B 309 ARG cc_start: 0.7208 (mtt-85) cc_final: 0.6876 (mmm-85) REVERT: B 339 ARG cc_start: 0.6872 (tpt170) cc_final: 0.6135 (mtp85) REVERT: B 451 MET cc_start: 0.7599 (mmt) cc_final: 0.7274 (ttt) outliers start: 3 outliers final: 1 residues processed: 153 average time/residue: 0.4695 time to fit residues: 91.3515 Evaluate side-chains 148 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.158405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.113051 restraints weight = 9282.156| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.32 r_work: 0.2960 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5830 Z= 0.188 Angle : 0.445 4.177 7946 Z= 0.235 Chirality : 0.035 0.129 978 Planarity : 0.004 0.045 974 Dihedral : 3.533 18.793 780 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.49 % Allowed : 16.99 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.32), residues: 726 helix: 2.65 (0.21), residues: 605 sheet: None (None), residues: 0 loop : -0.32 (0.64), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 394 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE B 389 TYR 0.007 0.001 TYR A 359 ARG 0.002 0.000 ARG B 35 =============================================================================== Job complete usr+sys time: 3077.68 seconds wall clock time: 54 minutes 47.40 seconds (3287.40 seconds total)