Starting phenix.real_space_refine on Sat Dec 9 16:02:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcb_21605/12_2023/6wcb_21605.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcb_21605/12_2023/6wcb_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_21605/12_2023/6wcb_21605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcb_21605/12_2023/6wcb_21605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcb_21605/12_2023/6wcb_21605.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcb_21605/12_2023/6wcb_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-1.21rc1-5172/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: 5.77, per 1000 atoms: 0.50 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: 9.85 Conformation dependent library (CDL) restraints added in 1.4 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: 0.95 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: 4.51 Time building geometry restraints manager: 10.05 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: 4909 14.97 - 29.94: 397 29.94 - 44.92: 93 44.92 - 59.89: 37 59.89 - 74.86: 6 Dihedral angle restraints: 5442 sinusoidal: 2850 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 5439 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: 0.780 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 44.350 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.790 ------------------------------------------------------------------------------- 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 : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 139 average time/residue: 0.3884 time to fit residues: 71.2535 Evaluate side-chains 115 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1377 time to fit residues: 2.1140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.7571 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5830 Z= 0.243 Angle : 0.476 4.681 7946 Z= 0.248 Chirality : 0.035 0.127 978 Planarity : 0.004 0.045 974 Dihedral : 3.280 18.630 780 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.62 % Allowed : 10.84 % Favored : 87.54 % 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: 1.86 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -2.00 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 324 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A 389 TYR 0.006 0.001 TYR A 160 ARG 0.003 0.000 ARG B 339 *********************** 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 129 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 125 average time/residue: 0.4851 time to fit residues: 75.5828 Evaluate side-chains 127 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2575 time to fit residues: 4.0270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- 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: 0.7641 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5830 Z= 0.249 Angle : 0.480 4.497 7946 Z= 0.257 Chirality : 0.036 0.129 978 Planarity : 0.004 0.024 974 Dihedral : 3.519 19.706 780 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.65 % Allowed : 11.81 % Favored : 87.54 % 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: 2.43 (0.32), residues: 726 helix: 2.16 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.08 (0.60), 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 0.010 0.001 PHE A 389 TYR 0.007 0.001 TYR A 359 ARG 0.007 0.001 ARG A 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 138 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 135 average time/residue: 0.4896 time to fit residues: 83.1672 Evaluate side-chains 131 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- 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: 0.7664 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5830 Z= 0.294 Angle : 0.489 4.395 7946 Z= 0.262 Chirality : 0.037 0.143 978 Planarity : 0.004 0.024 974 Dihedral : 3.593 19.793 780 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.29 % Allowed : 13.11 % 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: 2.51 (0.32), residues: 726 helix: 2.19 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -0.90 (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 0.011 0.001 PHE A 99 TYR 0.008 0.002 TYR A 359 ARG 0.003 0.000 ARG A 35 *********************** 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 141 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 135 average time/residue: 0.4963 time to fit residues: 82.5706 Evaluate side-chains 135 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1287 time to fit residues: 1.5611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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: 0.7669 moved from start: 0.3265 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= 0.262 Angle : 0.475 4.358 7946 Z= 0.253 Chirality : 0.037 0.171 978 Planarity : 0.003 0.026 974 Dihedral : 3.628 19.551 780 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.13 % Allowed : 13.92 % Favored : 84.95 % 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: 2.68 (0.32), residues: 726 helix: 2.30 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -0.83 (0.61), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 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 0.003 0.000 ARG B 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 147 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 141 average time/residue: 0.4922 time to fit residues: 86.2413 Evaluate side-chains 141 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1811 time to fit residues: 2.2750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 17 optimal weight: 0.0040 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 overall best weight: 4.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5830 Z= 0.241 Angle : 0.466 4.295 7946 Z= 0.247 Chirality : 0.036 0.124 978 Planarity : 0.003 0.026 974 Dihedral : 3.608 19.472 780 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.13 % Allowed : 14.24 % 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: 2.91 (0.32), residues: 726 helix: 2.46 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -0.77 (0.61), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 324 HIS 0.006 0.001 HIS A 328 PHE 0.010 0.001 PHE A 389 TYR 0.007 0.001 TYR A 359 ARG 0.002 0.000 ARG A 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: 7 poor density : 143 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 144 average time/residue: 0.4824 time to fit residues: 86.5316 Evaluate side-chains 143 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1371 time to fit residues: 1.3707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 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: 0.7652 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5830 Z= 0.179 Angle : 0.448 4.191 7946 Z= 0.235 Chirality : 0.035 0.123 978 Planarity : 0.003 0.027 974 Dihedral : 3.538 19.107 780 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: 3.15 (0.32), residues: 726 helix: 2.61 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.67 (0.62), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 324 HIS 0.005 0.001 HIS A 328 PHE 0.009 0.001 PHE B 389 TYR 0.009 0.001 TYR A 359 ARG 0.002 0.000 ARG B 375 *********************** 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 : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 144 average time/residue: 0.5784 time to fit residues: 103.7496 Evaluate side-chains 146 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1671 time to fit residues: 2.1244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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: 0.7643 moved from start: 0.3575 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= 0.164 Angle : 0.440 4.169 7946 Z= 0.231 Chirality : 0.035 0.123 978 Planarity : 0.003 0.029 974 Dihedral : 3.480 18.675 780 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.49 % Allowed : 15.53 % Favored : 83.98 % 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: 3.35 (0.32), residues: 726 helix: 2.73 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -0.49 (0.63), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 394 HIS 0.005 0.001 HIS A 328 PHE 0.009 0.001 PHE B 389 TYR 0.009 0.001 TYR A 359 ARG 0.005 0.000 ARG B 309 *********************** 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 150 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 147 average time/residue: 0.4952 time to fit residues: 90.2867 Evaluate side-chains 148 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1594 time to fit residues: 2.0027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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: 0.7643 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5830 Z= 0.169 Angle : 0.440 4.172 7946 Z= 0.230 Chirality : 0.035 0.124 978 Planarity : 0.003 0.028 974 Dihedral : 3.450 18.638 780 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % 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: 3.42 (0.33), residues: 726 helix: 2.76 (0.21), residues: 603 sheet: None (None), residues: 0 loop : -0.41 (0.64), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 394 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE B 389 TYR 0.009 0.001 TYR A 359 ARG 0.003 0.000 ARG B 309 *********************** 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 143 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.5141 time to fit residues: 91.2731 Evaluate side-chains 142 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 71 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5830 Z= 0.192 Angle : 0.444 4.212 7946 Z= 0.235 Chirality : 0.035 0.123 978 Planarity : 0.003 0.029 974 Dihedral : 3.462 18.734 780 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.32 % Allowed : 16.34 % 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: 3.40 (0.33), residues: 726 helix: 2.73 (0.21), residues: 603 sheet: None (None), residues: 0 loop : -0.35 (0.64), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 394 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A 389 TYR 0.007 0.001 TYR B 359 ARG 0.003 0.000 ARG B 309 ********************** 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 144 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 142 average time/residue: 0.5093 time to fit residues: 89.2667 Evaluate side-chains 144 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1401 time to fit residues: 1.6456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 50.0000 chunk 41 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.157733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.111444 restraints weight = 9308.963| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.36 r_work: 0.2937 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5830 Z= 0.178 Angle : 0.441 4.186 7946 Z= 0.233 Chirality : 0.035 0.123 978 Planarity : 0.003 0.029 974 Dihedral : 3.444 18.711 780 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 16.34 % 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: 3.44 (0.33), residues: 726 helix: 2.75 (0.21), residues: 603 sheet: None (None), residues: 0 loop : -0.32 (0.63), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 394 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A 389 TYR 0.007 0.001 TYR B 359 ARG 0.003 0.000 ARG B 309 =============================================================================== Job complete usr+sys time: 3178.48 seconds wall clock time: 56 minutes 52.50 seconds (3412.50 seconds total)