Starting phenix.real_space_refine on Fri Mar 15 12:47:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/03_2024/6wc9_21603.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/03_2024/6wc9_21603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/03_2024/6wc9_21603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/03_2024/6wc9_21603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/03_2024/6wc9_21603.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/03_2024/6wc9_21603.pdb" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.725 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 K 7 8.98 5 S 38 5.16 5 C 3754 2.51 5 N 938 2.21 5 O 1072 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 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 GLU 259": "OE1" <-> "OE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A GLU 293": "OE1" <-> "OE2" 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 ASP 371": "OD1" <-> "OD2" Residue "A GLU 374": "OE1" <-> "OE2" 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 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 GLU 259": "OE1" <-> "OE2" Residue "B ASP 283": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B GLU 293": "OE1" <-> "OE2" 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 ASP 371": "OD1" <-> "OD2" Residue "B GLU 374": "OE1" <-> "OE2" 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11713 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: {' K': 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: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Time building chain proxies: 5.52, per 1000 atoms: 0.47 Number of scatterers: 11713 At special positions: 0 Unit cell: (104.992, 71.264, 76.16, 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) K 7 19.00 S 38 16.00 O 1072 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: 12.24 Conformation dependent library (CDL) restraints added in 1.2 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 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 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 removed outlier: 3.632A pdb=" N VAL A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) 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 169 through 173 Processing helix chain 'A' and resid 257 through 284 removed outlier: 5.202A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 5.293A 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: 3.690A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 332 removed outlier: 3.555A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) 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 399 removed outlier: 3.673A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 439 removed outlier: 5.116A 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 508 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 removed outlier: 3.632A pdb=" N VAL B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) 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 169 through 173 Processing helix chain 'B' and resid 257 through 284 removed outlier: 5.202A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 5.293A 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: 3.690A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.555A pdb=" N PHE B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) 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 399 removed outlier: 3.672A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 439 removed outlier: 5.116A 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 476 466 hydrogen bonds defined for protein. 1368 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: 4.45 Time building geometry restraints manager: 12.38 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 - 1.22: 18 1.22 - 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 1.544 -0.209 1.32e-02 5.74e+03 2.51e+02 bond pdb=" C THR A 472 " pdb=" N LEU A 505 " ideal model delta sigma weight residual 1.335 1.544 -0.209 1.32e-02 5.74e+03 2.51e+02 bond pdb=" CB GLN B 65 " pdb=" CG GLN B 65 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CB GLN A 65 " pdb=" CG GLN A 65 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" C VAL B 409 " pdb=" O VAL B 409 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.92e-01 ... (remaining 11729 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.65: 167 106.65 - 113.50: 14026 113.50 - 120.35: 3840 120.35 - 127.20: 3164 127.20 - 134.05: 71 Bond angle restraints: 21268 Sorted by residual: angle pdb=" N PHE A 66 " pdb=" CA PHE A 66 " pdb=" C PHE A 66 " ideal model delta sigma weight residual 112.72 109.17 3.55 1.36e+00 5.41e-01 6.80e+00 angle pdb=" N PHE B 66 " pdb=" CA PHE B 66 " pdb=" C PHE B 66 " ideal model delta sigma weight residual 112.72 109.17 3.55 1.36e+00 5.41e-01 6.80e+00 angle pdb=" CA TRP A 394 " pdb=" CB TRP A 394 " pdb=" CG TRP A 394 " ideal model delta sigma weight residual 113.60 117.90 -4.30 1.90e+00 2.77e-01 5.13e+00 angle pdb=" CA TRP B 394 " pdb=" CB TRP B 394 " pdb=" CG TRP B 394 " ideal model delta sigma weight residual 113.60 117.87 -4.27 1.90e+00 2.77e-01 5.06e+00 angle pdb=" CD GLN A 65 " pdb=" CG GLN A 65 " pdb=" HG3 GLN A 65 " ideal model delta sigma weight residual 108.00 102.49 5.51 3.00e+00 1.11e-01 3.38e+00 ... (remaining 21263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 4861 16.03 - 32.06: 453 32.06 - 48.10: 128 48.10 - 64.13: 76 64.13 - 80.16: 10 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 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.73e+01 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 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLN A 65 " pdb=" C GLN A 65 " pdb=" N PHE A 66 " pdb=" CA PHE A 66 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 552 0.024 - 0.047: 237 0.047 - 0.071: 127 0.071 - 0.094: 30 0.094 - 0.118: 32 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 3.47e-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 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA PHE A 99 " pdb=" N PHE A 99 " pdb=" C PHE A 99 " pdb=" CB PHE A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 975 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 472 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" N LEU A 505 " -0.024 2.00e-02 2.50e+03 pdb=" CA LEU A 505 " 0.006 2.00e-02 2.50e+03 pdb=" H LEU A 505 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 307 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 308 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 307 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO B 308 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 308 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 308 " -0.017 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.31: 2625 2.31 - 3.02: 32108 3.02 - 3.72: 44488 3.72 - 4.43: 66574 4.43 - 5.14: 103031 Nonbonded interactions: 248826 Sorted by model distance: nonbonded pdb=" HE2 HIS A 95 " pdb=" OD1 ASN A 113 " model vdw 1.601 1.850 nonbonded pdb=" HE2 HIS B 95 " pdb=" OD1 ASN B 113 " model vdw 1.602 1.850 nonbonded pdb=" OD1 ASP A 266 " pdb=" HE1 TRP A 324 " model vdw 1.614 1.850 nonbonded pdb=" OD1 ASP B 266 " pdb=" HE1 TRP B 324 " model vdw 1.614 1.850 nonbonded pdb=" OE2 GLU A 282 " pdb=" HD1 HIS B 57 " model vdw 1.664 1.850 ... (remaining 248821 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: 8.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 35.020 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 46.150 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.006 0.209 5830 Z= 0.425 Angle : 0.537 4.603 7946 Z= 0.304 Chirality : 0.037 0.118 978 Planarity : 0.003 0.030 974 Dihedral : 15.749 80.161 2034 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.10 % Allowed : 15.37 % 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: -0.42 (0.30), residues: 726 helix: 0.31 (0.20), residues: 595 sheet: None (None), residues: 0 loop : -2.68 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 394 HIS 0.008 0.001 HIS B 328 PHE 0.013 0.001 PHE A 99 TYR 0.006 0.001 TYR B 359 ARG 0.004 0.000 ARG B 367 *********************** 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 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.871 Fit side-chains REVERT: A 34 GLN cc_start: 0.7379 (tt0) cc_final: 0.6849 (tm-30) REVERT: A 106 ASP cc_start: 0.8089 (p0) cc_final: 0.7549 (p0) REVERT: A 415 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7060 (mm-30) REVERT: A 444 SER cc_start: 0.6049 (OUTLIER) cc_final: 0.5758 (p) REVERT: B 34 GLN cc_start: 0.7379 (tt0) cc_final: 0.6851 (tm-30) REVERT: B 106 ASP cc_start: 0.8093 (p0) cc_final: 0.7539 (p0) REVERT: B 415 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7061 (mm-30) REVERT: B 434 PHE cc_start: 0.7190 (t80) cc_final: 0.6963 (t80) REVERT: B 444 SER cc_start: 0.6032 (OUTLIER) cc_final: 0.5755 (p) outliers start: 13 outliers final: 4 residues processed: 106 average time/residue: 2.1584 time to fit residues: 241.5308 Evaluate side-chains 87 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 444 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.0070 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 64 GLN A 360 GLN B 34 GLN B 64 GLN B 360 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1833 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= 0.216 Angle : 0.524 4.649 7946 Z= 0.282 Chirality : 0.038 0.142 978 Planarity : 0.004 0.037 974 Dihedral : 4.998 29.761 786 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.27 % Allowed : 17.80 % Favored : 79.94 % 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: 1.56 (0.32), residues: 726 helix: 1.66 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.95 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.017 0.002 PHE A 389 TYR 0.010 0.002 TYR B 81 ARG 0.002 0.000 ARG B 474 *********************** 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 105 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.936 Fit side-chains REVERT: A 34 GLN cc_start: 0.7423 (tt0) cc_final: 0.6790 (tm-30) REVERT: A 306 THR cc_start: 0.7319 (p) cc_final: 0.7027 (m) REVERT: A 408 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7461 (p) REVERT: A 415 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6885 (mm-30) REVERT: B 34 GLN cc_start: 0.7419 (tt0) cc_final: 0.6786 (tm-30) REVERT: B 306 THR cc_start: 0.7314 (p) cc_final: 0.7023 (m) REVERT: B 408 SER cc_start: 0.7925 (OUTLIER) cc_final: 0.7468 (p) REVERT: B 415 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6889 (mm-30) outliers start: 14 outliers final: 6 residues processed: 103 average time/residue: 2.0186 time to fit residues: 220.5889 Evaluate side-chains 87 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 408 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5830 Z= 0.271 Angle : 0.544 5.015 7946 Z= 0.293 Chirality : 0.039 0.155 978 Planarity : 0.004 0.040 974 Dihedral : 5.064 33.992 784 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.37 % Allowed : 15.86 % Favored : 79.77 % 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: 1.88 (0.31), residues: 726 helix: 1.86 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.72 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP B 324 HIS 0.006 0.002 HIS A 449 PHE 0.021 0.002 PHE A 99 TYR 0.012 0.002 TYR A 359 ARG 0.002 0.000 ARG A 72 *********************** 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 104 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 1.133 Fit side-chains REVERT: A 34 GLN cc_start: 0.7537 (tt0) cc_final: 0.6831 (tm-30) REVERT: A 152 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7784 (t) REVERT: A 415 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6969 (mm-30) REVERT: A 444 SER cc_start: 0.6179 (OUTLIER) cc_final: 0.5897 (p) REVERT: B 34 GLN cc_start: 0.7543 (tt0) cc_final: 0.6833 (tm-30) REVERT: B 152 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7776 (t) REVERT: B 408 SER cc_start: 0.7948 (OUTLIER) cc_final: 0.7518 (p) REVERT: B 415 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6978 (mm-30) REVERT: B 444 SER cc_start: 0.6165 (OUTLIER) cc_final: 0.5899 (p) outliers start: 27 outliers final: 12 residues processed: 98 average time/residue: 2.2003 time to fit residues: 228.0915 Evaluate side-chains 91 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 472 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5830 Z= 0.223 Angle : 0.507 4.463 7946 Z= 0.270 Chirality : 0.037 0.144 978 Planarity : 0.004 0.039 974 Dihedral : 4.942 36.189 784 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.40 % Allowed : 17.31 % Favored : 79.29 % 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: 2.30 (0.31), residues: 726 helix: 2.14 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.60 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.002 PHE B 99 TYR 0.011 0.002 TYR A 359 ARG 0.002 0.000 ARG A 506 *********************** 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 101 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7498 (tt0) cc_final: 0.6845 (tm-30) REVERT: A 152 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7788 (t) REVERT: A 306 THR cc_start: 0.7422 (p) cc_final: 0.7075 (m) REVERT: A 408 SER cc_start: 0.7917 (OUTLIER) cc_final: 0.7506 (p) REVERT: A 415 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7017 (mm-30) REVERT: B 34 GLN cc_start: 0.7496 (tt0) cc_final: 0.6840 (tm-30) REVERT: B 152 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7776 (t) REVERT: B 306 THR cc_start: 0.7426 (p) cc_final: 0.7082 (m) REVERT: B 408 SER cc_start: 0.7922 (OUTLIER) cc_final: 0.7512 (p) REVERT: B 415 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7024 (mm-30) outliers start: 21 outliers final: 9 residues processed: 93 average time/residue: 2.1800 time to fit residues: 214.0459 Evaluate side-chains 90 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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: 0.7711 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5830 Z= 0.232 Angle : 0.513 4.626 7946 Z= 0.275 Chirality : 0.038 0.148 978 Planarity : 0.004 0.039 974 Dihedral : 4.977 37.822 784 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.37 % Allowed : 16.50 % Favored : 79.13 % 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: 2.42 (0.31), residues: 726 helix: 2.23 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -1.55 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.021 0.002 PHE A 99 TYR 0.011 0.002 TYR B 359 ARG 0.001 0.000 ARG A 506 *********************** 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 108 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7513 (tt0) cc_final: 0.6854 (tm-30) REVERT: A 106 ASP cc_start: 0.8550 (p0) cc_final: 0.7968 (p0) REVERT: A 129 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7859 (mt) REVERT: A 152 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7806 (t) REVERT: A 306 THR cc_start: 0.7444 (p) cc_final: 0.7086 (m) REVERT: A 363 SER cc_start: 0.7483 (OUTLIER) cc_final: 0.7248 (m) REVERT: A 408 SER cc_start: 0.7915 (OUTLIER) cc_final: 0.7497 (p) REVERT: A 415 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7060 (mm-30) REVERT: A 444 SER cc_start: 0.6164 (OUTLIER) cc_final: 0.5878 (p) REVERT: B 34 GLN cc_start: 0.7513 (tt0) cc_final: 0.6853 (tm-30) REVERT: B 106 ASP cc_start: 0.8541 (p0) cc_final: 0.7956 (p0) REVERT: B 129 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7860 (mt) REVERT: B 152 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7794 (t) REVERT: B 306 THR cc_start: 0.7436 (p) cc_final: 0.7079 (m) REVERT: B 408 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7501 (p) REVERT: B 415 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7063 (mm-30) REVERT: B 444 SER cc_start: 0.6146 (OUTLIER) cc_final: 0.5878 (p) outliers start: 27 outliers final: 12 residues processed: 102 average time/residue: 1.9973 time to fit residues: 216.4983 Evaluate side-chains 102 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 472 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7709 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5830 Z= 0.224 Angle : 0.507 4.506 7946 Z= 0.271 Chirality : 0.037 0.146 978 Planarity : 0.004 0.039 974 Dihedral : 4.940 39.370 784 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.21 % Allowed : 16.67 % Favored : 79.13 % 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: 2.54 (0.32), residues: 726 helix: 2.29 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.45 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.020 0.002 PHE B 99 TYR 0.011 0.002 TYR A 359 ARG 0.001 0.000 ARG A 506 *********************** 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 109 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7522 (tt0) cc_final: 0.6861 (tm-30) REVERT: A 106 ASP cc_start: 0.8544 (p0) cc_final: 0.7959 (p0) REVERT: A 129 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7865 (mt) REVERT: A 152 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7796 (t) REVERT: A 306 THR cc_start: 0.7447 (p) cc_final: 0.7096 (m) REVERT: A 363 SER cc_start: 0.7441 (OUTLIER) cc_final: 0.7228 (m) REVERT: A 408 SER cc_start: 0.7935 (OUTLIER) cc_final: 0.7513 (p) REVERT: A 415 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7060 (mm-30) REVERT: A 444 SER cc_start: 0.6147 (OUTLIER) cc_final: 0.5856 (p) REVERT: B 34 GLN cc_start: 0.7515 (tt0) cc_final: 0.6855 (tm-30) REVERT: B 106 ASP cc_start: 0.8532 (p0) cc_final: 0.7947 (p0) REVERT: B 152 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7789 (t) REVERT: B 306 THR cc_start: 0.7446 (p) cc_final: 0.7095 (m) REVERT: B 363 SER cc_start: 0.7418 (OUTLIER) cc_final: 0.7203 (m) REVERT: B 408 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7519 (p) REVERT: B 415 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7072 (mm-30) outliers start: 26 outliers final: 9 residues processed: 102 average time/residue: 2.0199 time to fit residues: 218.5967 Evaluate side-chains 99 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.0270 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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: 0.7690 moved from start: 0.2796 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= 0.176 Angle : 0.476 4.427 7946 Z= 0.252 Chirality : 0.036 0.134 978 Planarity : 0.004 0.039 974 Dihedral : 4.753 39.694 784 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.88 % Allowed : 17.15 % Favored : 78.96 % 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: 2.89 (0.32), residues: 726 helix: 2.55 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -1.39 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.018 0.001 PHE B 99 TYR 0.009 0.002 TYR B 359 ARG 0.001 0.000 ARG A 506 *********************** 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 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7493 (tt0) cc_final: 0.6848 (tm-30) REVERT: A 106 ASP cc_start: 0.8473 (p0) cc_final: 0.7821 (p0) REVERT: A 152 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7788 (t) REVERT: A 306 THR cc_start: 0.7447 (p) cc_final: 0.7096 (m) REVERT: A 363 SER cc_start: 0.7394 (OUTLIER) cc_final: 0.7185 (m) REVERT: A 408 SER cc_start: 0.7921 (OUTLIER) cc_final: 0.7513 (p) REVERT: A 415 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7031 (mm-30) REVERT: A 444 SER cc_start: 0.6127 (OUTLIER) cc_final: 0.5828 (p) REVERT: B 34 GLN cc_start: 0.7500 (tt0) cc_final: 0.6857 (tm-30) REVERT: B 106 ASP cc_start: 0.8459 (p0) cc_final: 0.7807 (p0) REVERT: B 152 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7775 (t) REVERT: B 306 THR cc_start: 0.7446 (p) cc_final: 0.7097 (m) REVERT: B 363 SER cc_start: 0.7382 (OUTLIER) cc_final: 0.7162 (m) REVERT: B 408 SER cc_start: 0.7924 (OUTLIER) cc_final: 0.7518 (p) REVERT: B 415 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7051 (mm-30) REVERT: B 444 SER cc_start: 0.6111 (OUTLIER) cc_final: 0.5827 (p) outliers start: 24 outliers final: 10 residues processed: 101 average time/residue: 2.0000 time to fit residues: 213.9012 Evaluate side-chains 101 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.0060 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.2836 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= 0.182 Angle : 0.481 4.434 7946 Z= 0.256 Chirality : 0.036 0.137 978 Planarity : 0.004 0.039 974 Dihedral : 4.725 39.956 784 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.37 % Allowed : 16.83 % Favored : 78.80 % 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: 2.54 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.32 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.001 PHE B 99 TYR 0.010 0.002 TYR B 359 ARG 0.001 0.000 ARG A 506 *********************** 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 110 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7499 (tt0) cc_final: 0.6850 (tm-30) REVERT: A 106 ASP cc_start: 0.8491 (p0) cc_final: 0.7837 (p0) REVERT: A 152 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7794 (t) REVERT: A 306 THR cc_start: 0.7440 (p) cc_final: 0.7086 (m) REVERT: A 408 SER cc_start: 0.7932 (OUTLIER) cc_final: 0.7521 (p) REVERT: A 415 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7015 (mm-30) REVERT: A 444 SER cc_start: 0.6121 (OUTLIER) cc_final: 0.5808 (p) REVERT: B 34 GLN cc_start: 0.7511 (tt0) cc_final: 0.6865 (tm-30) REVERT: B 106 ASP cc_start: 0.8484 (p0) cc_final: 0.7825 (p0) REVERT: B 152 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7777 (t) REVERT: B 306 THR cc_start: 0.7444 (p) cc_final: 0.7094 (m) REVERT: B 408 SER cc_start: 0.7934 (OUTLIER) cc_final: 0.7524 (p) REVERT: B 415 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7027 (mm-30) REVERT: B 444 SER cc_start: 0.6101 (OUTLIER) cc_final: 0.5806 (p) outliers start: 27 outliers final: 13 residues processed: 104 average time/residue: 1.9845 time to fit residues: 218.8366 Evaluate side-chains 103 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 472 THR 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: 0.4980 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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: 0.7678 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5830 Z= 0.161 Angle : 0.465 4.603 7946 Z= 0.246 Chirality : 0.036 0.131 978 Planarity : 0.004 0.040 974 Dihedral : 4.591 40.093 784 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.75 % Allowed : 18.28 % Favored : 78.96 % 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: 3.12 (0.32), residues: 726 helix: 2.70 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -1.27 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.018 0.001 PHE B 99 TYR 0.009 0.002 TYR B 359 ARG 0.001 0.000 ARG A 506 *********************** 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 101 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7491 (tt0) cc_final: 0.6858 (tm-30) REVERT: A 106 ASP cc_start: 0.8460 (p0) cc_final: 0.7799 (p0) REVERT: A 306 THR cc_start: 0.7446 (p) cc_final: 0.7095 (m) REVERT: A 415 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7012 (mm-30) REVERT: B 34 GLN cc_start: 0.7496 (tt0) cc_final: 0.6852 (tm-30) REVERT: B 106 ASP cc_start: 0.8443 (p0) cc_final: 0.7785 (p0) REVERT: B 306 THR cc_start: 0.7440 (p) cc_final: 0.7088 (m) REVERT: B 415 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7031 (mm-30) REVERT: B 444 SER cc_start: 0.6109 (OUTLIER) cc_final: 0.5807 (p) outliers start: 17 outliers final: 13 residues processed: 96 average time/residue: 2.1348 time to fit residues: 216.6421 Evaluate side-chains 98 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 472 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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: 0.7697 moved from start: 0.2888 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= 0.203 Angle : 0.494 4.558 7946 Z= 0.264 Chirality : 0.037 0.142 978 Planarity : 0.004 0.039 974 Dihedral : 4.573 40.467 782 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.43 % Allowed : 18.77 % Favored : 78.80 % 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: 2.90 (0.32), residues: 726 helix: 2.50 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -1.13 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.021 0.002 PHE B 99 TYR 0.011 0.002 TYR B 359 ARG 0.001 0.000 ARG A 463 ********************** 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 99 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7497 (tt0) cc_final: 0.6840 (tm-30) REVERT: A 106 ASP cc_start: 0.8525 (p0) cc_final: 0.7932 (p0) REVERT: A 306 THR cc_start: 0.7437 (p) cc_final: 0.7076 (m) REVERT: A 415 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7026 (mm-30) REVERT: B 34 GLN cc_start: 0.7503 (tt0) cc_final: 0.6848 (tm-30) REVERT: B 106 ASP cc_start: 0.8515 (p0) cc_final: 0.7924 (p0) REVERT: B 306 THR cc_start: 0.7427 (p) cc_final: 0.7070 (m) REVERT: B 415 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7029 (mm-30) REVERT: B 444 SER cc_start: 0.6121 (OUTLIER) cc_final: 0.5816 (p) outliers start: 15 outliers final: 12 residues processed: 96 average time/residue: 2.1070 time to fit residues: 214.4652 Evaluate side-chains 97 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 472 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 3 optimal weight: 0.0270 chunk 41 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.168153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.147493 restraints weight = 13656.487| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 0.88 r_work: 0.3290 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5830 Z= 0.175 Angle : 0.474 4.595 7946 Z= 0.251 Chirality : 0.036 0.135 978 Planarity : 0.004 0.039 974 Dihedral : 4.498 40.672 782 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.91 % Allowed : 18.61 % Favored : 78.48 % 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: 3.07 (0.32), residues: 726 helix: 2.60 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -1.00 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.018 0.001 PHE B 99 TYR 0.009 0.002 TYR B 359 ARG 0.001 0.000 ARG A 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5392.46 seconds wall clock time: 95 minutes 19.58 seconds (5719.58 seconds total)