Starting phenix.real_space_refine on Sun Mar 10 23:55:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/03_2024/7p5m_13201.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/03_2024/7p5m_13201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/03_2024/7p5m_13201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/03_2024/7p5m_13201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/03_2024/7p5m_13201.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/03_2024/7p5m_13201.pdb" } resolution = 3.92 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4006 2.51 5 N 976 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6204 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3018 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 9, 'TRANS': 384} Chain breaks: 1 Chain: "B" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3018 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 9, 'TRANS': 384} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.86, per 1000 atoms: 0.62 Number of scatterers: 6204 At special positions: 0 Unit cell: (92.442, 70.308, 128.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1176 8.00 N 976 7.00 C 4006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 382 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 367 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 283 " " NAG A 602 " - " ASN A 31 " " NAG B 601 " - " ASN B 283 " " NAG B 602 " - " ASN B 31 " " NAG C 1 " - " ASN A 352 " " NAG D 1 " - " ASN A 129 " " NAG E 1 " - " ASN B 352 " " NAG F 1 " - " ASN B 129 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.3 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 Processing helix chain 'A' and resid 38 through 70 removed outlier: 3.660A pdb=" N ALA A 70 " --> pdb=" O TYR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 159 removed outlier: 4.199A pdb=" N LEU A 150 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 4.333A pdb=" N ALA A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 191 through 237 removed outlier: 3.502A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 276 removed outlier: 3.654A pdb=" N LEU A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 244 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 308 through 337 removed outlier: 3.971A pdb=" N VAL A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 341 through 365 Processing helix chain 'A' and resid 366 through 382 removed outlier: 4.426A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 414 removed outlier: 3.682A pdb=" N GLN A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Proline residue: A 411 - end of helix Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 38 through 70 removed outlier: 3.646A pdb=" N ALA B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 159 removed outlier: 4.245A pdb=" N LEU B 150 " --> pdb=" O MET B 146 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 4.284A pdb=" N ALA B 163 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 Processing helix chain 'B' and resid 191 through 237 removed outlier: 3.611A pdb=" N LEU B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 276 removed outlier: 3.739A pdb=" N LEU B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 244 " --> pdb=" O CYS B 240 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 308 through 337 removed outlier: 4.127A pdb=" N VAL B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 341 through 365 Processing helix chain 'B' and resid 366 through 383 removed outlier: 4.418A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 409 removed outlier: 3.543A pdb=" N GLN B 387 " --> pdb=" O TYR B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 562 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1918 1.34 - 1.46: 1290 1.46 - 1.58: 3062 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 6332 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.78e+00 ... (remaining 6327 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.34: 69 105.34 - 112.52: 3510 112.52 - 119.71: 1969 119.71 - 126.89: 3000 126.89 - 134.07: 82 Bond angle restraints: 8630 Sorted by residual: angle pdb=" C LEU B 282 " pdb=" N ASN B 283 " pdb=" CA ASN B 283 " ideal model delta sigma weight residual 122.65 116.56 6.09 1.60e+00 3.91e-01 1.45e+01 angle pdb=" C ASP B 166 " pdb=" N TYR B 167 " pdb=" CA TYR B 167 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C ASP A 166 " pdb=" N TYR A 167 " pdb=" CA TYR A 167 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C LEU A 282 " pdb=" N ASN A 283 " pdb=" CA ASN A 283 " ideal model delta sigma weight residual 122.38 116.47 5.91 1.81e+00 3.05e-01 1.07e+01 angle pdb=" N VAL B 23 " pdb=" CA VAL B 23 " pdb=" C VAL B 23 " ideal model delta sigma weight residual 113.71 110.95 2.76 9.50e-01 1.11e+00 8.42e+00 ... (remaining 8625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 3538 21.30 - 42.59: 249 42.59 - 63.89: 39 63.89 - 85.18: 6 85.18 - 106.48: 16 Dihedral angle restraints: 3848 sinusoidal: 1562 harmonic: 2286 Sorted by residual: dihedral pdb=" CB CYS A 300 " pdb=" SG CYS A 300 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual 93.00 61.58 31.42 1 1.00e+01 1.00e-02 1.41e+01 dihedral pdb=" C2 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" O4 NAG C 2 " ideal model delta sinusoidal sigma weight residual 175.11 68.63 106.48 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C2 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" C5 NAG C 2 " ideal model delta sinusoidal sigma weight residual 53.78 -52.46 106.24 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 3845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 901 0.051 - 0.102: 148 0.102 - 0.152: 11 0.152 - 0.203: 4 0.203 - 0.254: 2 Chirality restraints: 1066 Sorted by residual: chirality pdb=" CA ASN A 283 " pdb=" N ASN A 283 " pdb=" C ASN A 283 " pdb=" CB ASN A 283 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 129 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 283 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1063 not shown) Planarity restraints: 1058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 283 " 0.001 2.00e-02 2.50e+03 3.05e-02 1.16e+01 pdb=" CG ASN A 283 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 283 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN A 283 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 167 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C TYR B 167 " -0.058 2.00e-02 2.50e+03 pdb=" O TYR B 167 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 168 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 167 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C TYR A 167 " 0.055 2.00e-02 2.50e+03 pdb=" O TYR A 167 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 168 " -0.019 2.00e-02 2.50e+03 ... (remaining 1055 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 823 2.75 - 3.29: 6592 3.29 - 3.82: 10801 3.82 - 4.36: 11266 4.36 - 4.90: 20145 Nonbonded interactions: 49627 Sorted by model distance: nonbonded pdb=" O TYR A 41 " pdb=" OG SER A 44 " model vdw 2.209 2.440 nonbonded pdb=" O LEU A 154 " pdb=" OG SER A 158 " model vdw 2.234 2.440 nonbonded pdb=" OE2 GLU A 151 " pdb=" NE2 GLN A 175 " model vdw 2.248 2.520 nonbonded pdb=" OD1 ASN B 31 " pdb=" OG1 THR B 33 " model vdw 2.249 2.440 nonbonded pdb=" OD2 ASP A 38 " pdb=" OG SER A 40 " model vdw 2.259 2.440 ... (remaining 49622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.010 Extract box with map and model: 2.700 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.780 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.003 0.033 6332 Z= 0.225 Angle : 0.597 7.966 8630 Z= 0.297 Chirality : 0.039 0.254 1066 Planarity : 0.004 0.052 1050 Dihedral : 16.498 106.479 2368 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.52 (0.30), residues: 780 helix: 2.66 (0.19), residues: 662 sheet: None (None), residues: 0 loop : 0.33 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 414 HIS 0.003 0.001 HIS B 18 PHE 0.020 0.001 PHE B 395 TYR 0.015 0.001 TYR B 216 ARG 0.004 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7340 (t0) cc_final: 0.7015 (t0) REVERT: A 406 MET cc_start: 0.8207 (tmm) cc_final: 0.7957 (tmm) REVERT: B 127 ASP cc_start: 0.7753 (t0) cc_final: 0.7064 (t0) REVERT: B 166 ASP cc_start: 0.7517 (p0) cc_final: 0.7070 (m-30) REVERT: B 210 TYR cc_start: 0.6851 (t80) cc_final: 0.6566 (t80) REVERT: B 341 GLU cc_start: 0.8057 (pp20) cc_final: 0.7557 (pp20) REVERT: B 406 MET cc_start: 0.8378 (tmm) cc_final: 0.8087 (tmm) REVERT: B 412 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7477 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1471 time to fit residues: 41.0751 Evaluate side-chains 188 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 0.0170 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 70 optimal weight: 0.0060 overall best weight: 0.3834 ------------------------------------------------------------------------------- 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: 0.7619 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6332 Z= 0.158 Angle : 0.562 7.795 8630 Z= 0.276 Chirality : 0.038 0.198 1066 Planarity : 0.004 0.052 1050 Dihedral : 11.609 76.880 1090 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.53 % Allowed : 12.08 % Favored : 86.39 % 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: 3.74 (0.29), residues: 780 helix: 2.80 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 0.35 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 12 HIS 0.001 0.000 HIS B 416 PHE 0.014 0.001 PHE A 47 TYR 0.011 0.001 TYR B 374 ARG 0.003 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7443 (t0) cc_final: 0.6971 (t0) REVERT: A 412 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7057 (ttm-80) REVERT: B 127 ASP cc_start: 0.7763 (t0) cc_final: 0.7073 (t0) REVERT: B 166 ASP cc_start: 0.7694 (p0) cc_final: 0.7212 (p0) REVERT: B 210 TYR cc_start: 0.6816 (t80) cc_final: 0.6480 (t80) REVERT: B 325 GLN cc_start: 0.7430 (mp10) cc_final: 0.7151 (mp10) REVERT: B 341 GLU cc_start: 0.8096 (pp20) cc_final: 0.7552 (pp20) REVERT: B 406 MET cc_start: 0.8357 (tmm) cc_final: 0.8121 (tmm) REVERT: B 412 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7261 (ttm170) outliers start: 10 outliers final: 10 residues processed: 210 average time/residue: 0.1462 time to fit residues: 41.8904 Evaluate side-chains 212 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 202 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 408 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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: 0.7664 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6332 Z= 0.208 Angle : 0.575 7.736 8630 Z= 0.281 Chirality : 0.038 0.180 1066 Planarity : 0.004 0.054 1050 Dihedral : 8.320 57.378 1090 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.91 % Allowed : 16.36 % Favored : 80.73 % 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: 3.72 (0.29), residues: 780 helix: 2.80 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 0.35 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 12 HIS 0.002 0.001 HIS A 359 PHE 0.021 0.001 PHE A 47 TYR 0.010 0.001 TYR B 374 ARG 0.004 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 223 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7534 (t0) cc_final: 0.6831 (t0) REVERT: A 412 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7320 (ttm170) REVERT: B 127 ASP cc_start: 0.7787 (t0) cc_final: 0.7099 (t0) REVERT: B 166 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7234 (p0) REVERT: B 210 TYR cc_start: 0.6852 (t80) cc_final: 0.6537 (t80) REVERT: B 325 GLN cc_start: 0.7573 (mp10) cc_final: 0.7298 (mp10) REVERT: B 341 GLU cc_start: 0.8130 (pp20) cc_final: 0.7534 (pp20) REVERT: B 406 MET cc_start: 0.8463 (tmm) cc_final: 0.8183 (tmm) REVERT: B 412 ARG cc_start: 0.8098 (mtt180) cc_final: 0.7265 (ttm170) outliers start: 19 outliers final: 14 residues processed: 226 average time/residue: 0.1655 time to fit residues: 51.5921 Evaluate side-chains 221 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 206 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 408 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7649 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6332 Z= 0.182 Angle : 0.564 7.191 8630 Z= 0.273 Chirality : 0.038 0.255 1066 Planarity : 0.004 0.055 1050 Dihedral : 6.645 56.190 1090 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.75 % Allowed : 20.95 % Favored : 76.30 % 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: 3.82 (0.29), residues: 780 helix: 2.89 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 0.14 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 12 HIS 0.002 0.000 HIS B 18 PHE 0.020 0.001 PHE B 173 TYR 0.017 0.001 TYR A 109 ARG 0.005 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7501 (t0) cc_final: 0.6662 (t0) REVERT: A 412 ARG cc_start: 0.7853 (mtt180) cc_final: 0.7229 (ttm170) REVERT: B 127 ASP cc_start: 0.7806 (t0) cc_final: 0.7077 (t0) REVERT: B 166 ASP cc_start: 0.8141 (p0) cc_final: 0.7609 (p0) REVERT: B 210 TYR cc_start: 0.6811 (t80) cc_final: 0.6489 (t80) REVERT: B 273 PHE cc_start: 0.8268 (t80) cc_final: 0.8055 (t80) REVERT: B 325 GLN cc_start: 0.7536 (mp10) cc_final: 0.7228 (mp10) REVERT: B 341 GLU cc_start: 0.8128 (pp20) cc_final: 0.7612 (pp20) REVERT: B 406 MET cc_start: 0.8557 (tmm) cc_final: 0.8314 (tmm) REVERT: B 412 ARG cc_start: 0.8061 (mtt180) cc_final: 0.7121 (ttm170) outliers start: 18 outliers final: 15 residues processed: 224 average time/residue: 0.1441 time to fit residues: 44.0487 Evaluate side-chains 226 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 211 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 408 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- 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: 0.7696 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6332 Z= 0.234 Angle : 0.586 7.515 8630 Z= 0.287 Chirality : 0.039 0.253 1066 Planarity : 0.004 0.055 1050 Dihedral : 6.210 54.682 1090 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.67 % Allowed : 21.71 % Favored : 74.62 % 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: 3.77 (0.29), residues: 780 helix: 2.84 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 0.29 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 12 HIS 0.003 0.001 HIS B 359 PHE 0.023 0.002 PHE B 173 TYR 0.010 0.001 TYR A 109 ARG 0.002 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 214 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7478 (t0) cc_final: 0.6619 (t70) REVERT: A 412 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7244 (ttm170) REVERT: B 166 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7802 (p0) REVERT: B 210 TYR cc_start: 0.6865 (t80) cc_final: 0.6586 (t80) REVERT: B 341 GLU cc_start: 0.8160 (pp20) cc_final: 0.7580 (pp20) REVERT: B 406 MET cc_start: 0.8698 (tmm) cc_final: 0.8417 (tmm) outliers start: 24 outliers final: 20 residues processed: 219 average time/residue: 0.1462 time to fit residues: 43.9681 Evaluate side-chains 229 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 408 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7673 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6332 Z= 0.185 Angle : 0.563 8.740 8630 Z= 0.272 Chirality : 0.038 0.242 1066 Planarity : 0.004 0.054 1050 Dihedral : 5.964 52.106 1090 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.82 % Allowed : 22.94 % Favored : 73.24 % 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: 3.89 (0.29), residues: 780 helix: 2.92 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 0.27 (0.60), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 12 HIS 0.001 0.000 HIS B 359 PHE 0.022 0.002 PHE B 173 TYR 0.011 0.001 TYR A 374 ARG 0.003 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 213 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7570 (t0) cc_final: 0.6865 (t70) REVERT: A 412 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7248 (ttm170) REVERT: B 166 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7757 (p0) REVERT: B 210 TYR cc_start: 0.6966 (t80) cc_final: 0.6640 (t80) REVERT: B 325 GLN cc_start: 0.7650 (mp10) cc_final: 0.6955 (mp10) REVERT: B 341 GLU cc_start: 0.8071 (pp20) cc_final: 0.7505 (pp20) REVERT: B 406 MET cc_start: 0.8747 (tmm) cc_final: 0.8344 (tmm) outliers start: 25 outliers final: 22 residues processed: 220 average time/residue: 0.1381 time to fit residues: 42.1887 Evaluate side-chains 232 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 209 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 408 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0020 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6332 Z= 0.165 Angle : 0.568 8.023 8630 Z= 0.271 Chirality : 0.037 0.233 1066 Planarity : 0.004 0.055 1050 Dihedral : 5.762 49.625 1090 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.98 % Allowed : 23.09 % Favored : 72.94 % 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: 3.99 (0.29), residues: 780 helix: 2.98 (0.19), residues: 668 sheet: None (None), residues: 0 loop : 0.30 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 12 HIS 0.001 0.000 HIS B 22 PHE 0.020 0.002 PHE A 47 TYR 0.010 0.001 TYR A 374 ARG 0.002 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7564 (t0) cc_final: 0.6860 (t70) REVERT: A 412 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7208 (ttm170) REVERT: B 150 LEU cc_start: 0.8180 (tp) cc_final: 0.7849 (tt) REVERT: B 166 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7678 (p0) REVERT: B 210 TYR cc_start: 0.7025 (t80) cc_final: 0.6685 (t80) REVERT: B 325 GLN cc_start: 0.7668 (mp10) cc_final: 0.7006 (mp10) REVERT: B 341 GLU cc_start: 0.8042 (pp20) cc_final: 0.7494 (pp20) outliers start: 26 outliers final: 23 residues processed: 226 average time/residue: 0.1427 time to fit residues: 44.8754 Evaluate side-chains 234 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 408 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6332 Z= 0.192 Angle : 0.586 9.000 8630 Z= 0.278 Chirality : 0.038 0.234 1066 Planarity : 0.004 0.055 1050 Dihedral : 5.668 48.065 1090 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.89 % Allowed : 22.48 % Favored : 72.63 % 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: 3.96 (0.29), residues: 780 helix: 2.95 (0.19), residues: 668 sheet: None (None), residues: 0 loop : 0.39 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 257 HIS 0.001 0.000 HIS B 359 PHE 0.023 0.001 PHE B 173 TYR 0.010 0.001 TYR A 374 ARG 0.002 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 216 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7616 (t0) cc_final: 0.6887 (t70) REVERT: A 412 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7159 (ttm170) REVERT: B 166 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7706 (p0) REVERT: B 210 TYR cc_start: 0.6850 (t80) cc_final: 0.6574 (t80) REVERT: B 325 GLN cc_start: 0.7640 (mp10) cc_final: 0.6975 (mp10) REVERT: B 341 GLU cc_start: 0.8036 (pp20) cc_final: 0.7537 (pp20) REVERT: B 375 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8581 (mt) outliers start: 32 outliers final: 27 residues processed: 228 average time/residue: 0.1782 time to fit residues: 56.1000 Evaluate side-chains 243 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 214 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 408 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6332 Z= 0.189 Angle : 0.598 8.746 8630 Z= 0.283 Chirality : 0.038 0.232 1066 Planarity : 0.004 0.055 1050 Dihedral : 5.571 46.636 1090 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.74 % Allowed : 23.24 % Favored : 72.02 % 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: 3.98 (0.29), residues: 780 helix: 2.96 (0.19), residues: 668 sheet: None (None), residues: 0 loop : 0.44 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 12 HIS 0.001 0.000 HIS B 359 PHE 0.020 0.002 PHE A 47 TYR 0.010 0.001 TYR A 374 ARG 0.003 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7606 (t0) cc_final: 0.6884 (t70) REVERT: A 337 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: A 412 ARG cc_start: 0.7633 (mtt180) cc_final: 0.7054 (ttm170) REVERT: B 166 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7711 (p0) REVERT: B 210 TYR cc_start: 0.6923 (t80) cc_final: 0.6621 (t80) REVERT: B 325 GLN cc_start: 0.7664 (mp10) cc_final: 0.6958 (mp10) REVERT: B 337 PHE cc_start: 0.6382 (m-10) cc_final: 0.5975 (m-10) REVERT: B 341 GLU cc_start: 0.7997 (pp20) cc_final: 0.7555 (pp20) REVERT: B 375 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8594 (mt) outliers start: 31 outliers final: 26 residues processed: 226 average time/residue: 0.1366 time to fit residues: 42.5400 Evaluate side-chains 240 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 408 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6332 Z= 0.198 Angle : 0.624 10.778 8630 Z= 0.291 Chirality : 0.038 0.233 1066 Planarity : 0.004 0.055 1050 Dihedral : 5.552 46.149 1090 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.43 % Allowed : 23.55 % Favored : 72.02 % 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: 3.97 (0.29), residues: 780 helix: 2.95 (0.19), residues: 668 sheet: None (None), residues: 0 loop : 0.44 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 12 HIS 0.001 0.000 HIS B 359 PHE 0.018 0.001 PHE A 47 TYR 0.010 0.001 TYR A 374 ARG 0.003 0.000 ARG A 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 210 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.7606 (t0) cc_final: 0.6891 (t70) REVERT: A 337 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: A 412 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7062 (ttm170) REVERT: B 166 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7732 (p0) REVERT: B 210 TYR cc_start: 0.6782 (t80) cc_final: 0.6556 (t80) REVERT: B 325 GLN cc_start: 0.7644 (mp10) cc_final: 0.6955 (mp10) REVERT: B 337 PHE cc_start: 0.6444 (m-10) cc_final: 0.6064 (m-10) REVERT: B 341 GLU cc_start: 0.7902 (pp20) cc_final: 0.7590 (pp20) REVERT: B 375 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8594 (mt) outliers start: 29 outliers final: 25 residues processed: 223 average time/residue: 0.1420 time to fit residues: 43.4525 Evaluate side-chains 239 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 408 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.171590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.147058 restraints weight = 8671.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.150861 restraints weight = 5094.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.153351 restraints weight = 3529.992| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6332 Z= 0.196 Angle : 0.623 11.081 8630 Z= 0.290 Chirality : 0.038 0.234 1066 Planarity : 0.004 0.055 1050 Dihedral : 5.506 46.008 1090 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.28 % Allowed : 24.16 % Favored : 71.56 % 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: 3.94 (0.29), residues: 780 helix: 2.93 (0.19), residues: 668 sheet: None (None), residues: 0 loop : 0.42 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 12 HIS 0.001 0.000 HIS B 359 PHE 0.017 0.002 PHE A 47 TYR 0.010 0.001 TYR A 374 ARG 0.006 0.001 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1490.16 seconds wall clock time: 27 minutes 48.70 seconds (1668.70 seconds total)