Starting phenix.real_space_refine on Fri Aug 2 19:34:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttf_41606/08_2024/8ttf_41606.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttf_41606/08_2024/8ttf_41606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttf_41606/08_2024/8ttf_41606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttf_41606/08_2024/8ttf_41606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttf_41606/08_2024/8ttf_41606.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttf_41606/08_2024/8ttf_41606.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.055 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 27 5.16 5 C 3121 2.51 5 N 755 2.21 5 O 860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 144": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4763 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2987 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain: "C" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "D" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 786 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Time building chain proxies: 3.36, per 1000 atoms: 0.71 Number of scatterers: 4763 At special positions: 0 Unit cell: (59.924, 74.272, 104.656, 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 27 16.00 O 860 8.00 N 755 7.00 C 3121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 112 " distance=2.04 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: 1.60 Conformation dependent library (CDL) restraints added in 860.0 milliseconds 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 56.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.552A pdb=" N ILE A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 25 through 33 removed outlier: 3.579A pdb=" N TYR A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS A 31 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 33 " --> pdb=" O TYR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 65 removed outlier: 3.590A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 67 through 88 Processing helix chain 'A' and resid 90 through 120 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.609A pdb=" N GLN A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 125' Processing helix chain 'A' and resid 126 through 152 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 156 through 177 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 233 removed outlier: 3.886A pdb=" N GLN A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 264 removed outlier: 3.728A pdb=" N TYR A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 288 removed outlier: 3.679A pdb=" N VAL A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 308 removed outlier: 4.059A pdb=" N ILE A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.551A pdb=" N ALA A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 354 Proline residue: A 344 - end of helix removed outlier: 3.862A pdb=" N PHE A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 386 removed outlier: 3.820A pdb=" N GLN A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 33 Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 86 removed outlier: 5.628A pdb=" N TRP C 73 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG C 64 " --> pdb=" O TRP C 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 129 through 132 Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 31 Processing sheet with id=AA5, first strand: chain 'D' and resid 34 through 36 removed outlier: 7.110A pdb=" N LEU D 35 " --> pdb=" O GLU D 129 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 126 " --> pdb=" O TYR D 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 110 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP D 59 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 34 through 36 removed outlier: 7.110A pdb=" N LEU D 35 " --> pdb=" O GLU D 129 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 126 " --> pdb=" O TYR D 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 110 " --> pdb=" O THR D 126 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 867 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: 1.37 Time building geometry restraints manager: 1.81 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: 1443 1.34 - 1.46: 1277 1.46 - 1.58: 2110 1.58 - 1.70: 1 1.70 - 1.82: 49 Bond restraints: 4880 Sorted by residual: bond pdb=" CB PRO C 140 " pdb=" CG PRO C 140 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.23e+00 bond pdb=" CA GLU A 192 " pdb=" CB GLU A 192 " ideal model delta sigma weight residual 1.522 1.531 -0.009 7.00e-03 2.04e+04 1.58e+00 bond pdb=" CG1 ILE A 15 " pdb=" CD1 ILE A 15 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.76e-01 bond pdb=" C PHE C 134 " pdb=" N TYR C 135 " ideal model delta sigma weight residual 1.330 1.341 -0.011 1.23e-02 6.61e+03 7.87e-01 bond pdb=" CG PRO C 140 " pdb=" CD PRO C 140 " ideal model delta sigma weight residual 1.503 1.475 0.028 3.40e-02 8.65e+02 6.70e-01 ... (remaining 4875 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.96: 105 105.96 - 112.96: 2589 112.96 - 119.97: 1651 119.97 - 126.97: 2219 126.97 - 133.97: 50 Bond angle restraints: 6614 Sorted by residual: angle pdb=" CA PRO C 140 " pdb=" N PRO C 140 " pdb=" CD PRO C 140 " ideal model delta sigma weight residual 112.00 105.31 6.69 1.40e+00 5.10e-01 2.28e+01 angle pdb=" C TYR C 133 " pdb=" N PHE C 134 " pdb=" CA PHE C 134 " ideal model delta sigma weight residual 123.05 129.10 -6.05 1.57e+00 4.06e-01 1.48e+01 angle pdb=" C LEU A 191 " pdb=" N GLU A 192 " pdb=" CA GLU A 192 " ideal model delta sigma weight residual 122.83 126.38 -3.55 1.08e+00 8.57e-01 1.08e+01 angle pdb=" CB MET A 95 " pdb=" CG MET A 95 " pdb=" SD MET A 95 " ideal model delta sigma weight residual 112.70 121.42 -8.72 3.00e+00 1.11e-01 8.46e+00 angle pdb=" N PRO C 140 " pdb=" CD PRO C 140 " pdb=" CG PRO C 140 " ideal model delta sigma weight residual 103.20 98.96 4.24 1.50e+00 4.44e-01 8.00e+00 ... (remaining 6609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 2537 16.70 - 33.40: 244 33.40 - 50.10: 43 50.10 - 66.80: 4 66.80 - 83.50: 6 Dihedral angle restraints: 2834 sinusoidal: 1062 harmonic: 1772 Sorted by residual: dihedral pdb=" CA TRP C 131 " pdb=" C TRP C 131 " pdb=" N TYR C 132 " pdb=" CA TYR C 132 " ideal model delta harmonic sigma weight residual 180.00 157.75 22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLU A 192 " pdb=" C GLU A 192 " pdb=" N PRO A 193 " pdb=" CA PRO A 193 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA TYR A 235 " pdb=" C TYR A 235 " pdb=" N SER A 236 " pdb=" CA SER A 236 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 588 0.046 - 0.092: 136 0.092 - 0.139: 29 0.139 - 0.185: 1 0.185 - 0.231: 1 Chirality restraints: 755 Sorted by residual: chirality pdb=" CA PHE C 134 " pdb=" N PHE C 134 " pdb=" C PHE C 134 " pdb=" CB PHE C 134 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA LEU A 26 " pdb=" N LEU A 26 " pdb=" C LEU A 26 " pdb=" CB LEU A 26 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA ASN A 234 " pdb=" N ASN A 234 " pdb=" C ASN A 234 " pdb=" CB ASN A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 752 not shown) Planarity restraints: 816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 139 " 0.053 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO C 140 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 140 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 140 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 27 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 133 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C TYR C 133 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR C 133 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE C 134 " 0.009 2.00e-02 2.50e+03 ... (remaining 813 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 78 2.69 - 3.25: 4748 3.25 - 3.80: 7620 3.80 - 4.35: 9371 4.35 - 4.90: 15937 Nonbonded interactions: 37754 Sorted by model distance: nonbonded pdb=" OG SER C 76 " pdb=" OG SER C 85 " model vdw 2.144 3.040 nonbonded pdb=" OG SER C 57 " pdb=" OE1 GLU C 128 " model vdw 2.270 3.040 nonbonded pdb=" OE1 GLN D 30 " pdb=" OG1 THR D 126 " model vdw 2.312 3.040 nonbonded pdb=" O SER A 81 " pdb=" OG SER A 97 " model vdw 2.328 3.040 nonbonded pdb=" NZ LYS A 68 " pdb=" O ILE A 177 " model vdw 2.335 3.120 ... (remaining 37749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 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 0.103 4880 Z= 0.174 Angle : 0.599 8.724 6614 Z= 0.319 Chirality : 0.041 0.231 755 Planarity : 0.005 0.077 816 Dihedral : 13.410 83.495 1702 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.37 (0.36), residues: 615 helix: 1.69 (0.31), residues: 331 sheet: 0.62 (0.51), residues: 122 loop : -0.41 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 73 HIS 0.004 0.001 HIS C 61 PHE 0.012 0.001 PHE A 10 TYR 0.024 0.002 TYR A 235 ARG 0.002 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.501 Fit side-chains REVERT: A 231 ASP cc_start: 0.8218 (t70) cc_final: 0.7974 (t0) REVERT: A 308 MET cc_start: 0.6697 (mmt) cc_final: 0.6378 (tpp) REVERT: A 346 ILE cc_start: 0.8752 (mm) cc_final: 0.8513 (mm) REVERT: A 385 GLU cc_start: 0.5275 (mp0) cc_final: 0.5061 (mp0) REVERT: C 125 MET cc_start: 0.8044 (mtm) cc_final: 0.7776 (mtm) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1790 time to fit residues: 24.7020 Evaluate side-chains 97 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4880 Z= 0.188 Angle : 0.608 11.595 6614 Z= 0.300 Chirality : 0.043 0.202 755 Planarity : 0.004 0.037 816 Dihedral : 4.262 22.203 660 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.16 % Allowed : 11.41 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.54 (0.36), residues: 615 helix: 1.94 (0.31), residues: 327 sheet: 0.65 (0.51), residues: 122 loop : -0.48 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 73 HIS 0.003 0.001 HIS A 155 PHE 0.025 0.001 PHE C 134 TYR 0.022 0.002 TYR A 235 ARG 0.002 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.503 Fit side-chains REVERT: A 231 ASP cc_start: 0.8264 (t70) cc_final: 0.7982 (t0) REVERT: A 308 MET cc_start: 0.6822 (mmt) cc_final: 0.6481 (tpp) REVERT: A 341 PHE cc_start: 0.7798 (t80) cc_final: 0.7285 (t80) REVERT: D 127 LYS cc_start: 0.8410 (ttpp) cc_final: 0.8074 (tmmt) outliers start: 6 outliers final: 2 residues processed: 105 average time/residue: 0.1681 time to fit residues: 22.5170 Evaluate side-chains 97 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 379 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4880 Z= 0.167 Angle : 0.580 8.093 6614 Z= 0.286 Chirality : 0.042 0.198 755 Planarity : 0.004 0.033 816 Dihedral : 4.108 22.160 660 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.32 % Allowed : 15.28 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.64 (0.36), residues: 615 helix: 2.01 (0.31), residues: 327 sheet: 0.67 (0.50), residues: 122 loop : -0.40 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 136 HIS 0.003 0.001 HIS C 61 PHE 0.016 0.001 PHE A 341 TYR 0.018 0.001 TYR A 235 ARG 0.002 0.000 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.508 Fit side-chains REVERT: A 308 MET cc_start: 0.6820 (mmt) cc_final: 0.6480 (tpp) REVERT: A 341 PHE cc_start: 0.7856 (t80) cc_final: 0.7584 (t80) REVERT: D 127 LYS cc_start: 0.8416 (ttpp) cc_final: 0.8036 (tmmt) outliers start: 12 outliers final: 5 residues processed: 102 average time/residue: 0.1624 time to fit residues: 21.1798 Evaluate side-chains 100 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4880 Z= 0.176 Angle : 0.577 8.618 6614 Z= 0.286 Chirality : 0.042 0.193 755 Planarity : 0.004 0.031 816 Dihedral : 4.072 22.413 660 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.51 % Allowed : 16.83 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.69 (0.36), residues: 615 helix: 2.07 (0.31), residues: 327 sheet: 0.72 (0.50), residues: 122 loop : -0.46 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 136 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.001 PHE C 134 TYR 0.019 0.002 TYR A 235 ARG 0.002 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.487 Fit side-chains REVERT: A 231 ASP cc_start: 0.8300 (t70) cc_final: 0.8021 (t0) REVERT: A 308 MET cc_start: 0.6891 (mmt) cc_final: 0.6578 (tpp) REVERT: D 85 ARG cc_start: 0.6281 (ptt180) cc_final: 0.6044 (ptt180) REVERT: D 106 ASP cc_start: 0.7452 (m-30) cc_final: 0.7180 (m-30) REVERT: D 127 LYS cc_start: 0.8318 (ttpp) cc_final: 0.7944 (tmmt) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 0.1609 time to fit residues: 22.7884 Evaluate side-chains 106 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain D residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7519 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4880 Z= 0.169 Angle : 0.566 8.570 6614 Z= 0.284 Chirality : 0.042 0.191 755 Planarity : 0.004 0.031 816 Dihedral : 4.049 22.533 660 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.71 % Allowed : 17.02 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.67 (0.36), residues: 615 helix: 2.04 (0.30), residues: 329 sheet: 0.79 (0.50), residues: 122 loop : -0.54 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 136 HIS 0.002 0.001 HIS A 155 PHE 0.016 0.001 PHE C 134 TYR 0.020 0.001 TYR A 235 ARG 0.002 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.534 Fit side-chains REVERT: A 308 MET cc_start: 0.6856 (mmt) cc_final: 0.6566 (tpp) REVERT: D 106 ASP cc_start: 0.7539 (m-30) cc_final: 0.7310 (m-30) REVERT: D 127 LYS cc_start: 0.8306 (ttpp) cc_final: 0.7919 (tmmt) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 0.1627 time to fit residues: 22.3976 Evaluate side-chains 108 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain D residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.0770 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- 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: 0.7623 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 4880 Z= 0.302 Angle : 0.640 8.410 6614 Z= 0.325 Chirality : 0.045 0.204 755 Planarity : 0.004 0.034 816 Dihedral : 4.203 22.529 660 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.87 % Allowed : 19.15 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.42 (0.36), residues: 615 helix: 1.75 (0.30), residues: 329 sheet: 0.78 (0.50), residues: 122 loop : -0.52 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 136 HIS 0.003 0.001 HIS A 155 PHE 0.019 0.002 PHE C 134 TYR 0.018 0.002 TYR C 133 ARG 0.003 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.521 Fit side-chains REVERT: A 125 LYS cc_start: 0.6701 (mttt) cc_final: 0.6461 (mmtm) REVERT: A 308 MET cc_start: 0.7014 (mmt) cc_final: 0.6727 (tpp) REVERT: D 106 ASP cc_start: 0.7508 (m-30) cc_final: 0.6964 (m-30) REVERT: D 127 LYS cc_start: 0.8330 (ttpp) cc_final: 0.7904 (tmmt) outliers start: 20 outliers final: 14 residues processed: 120 average time/residue: 0.1678 time to fit residues: 25.6400 Evaluate side-chains 116 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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: 0.7556 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4880 Z= 0.187 Angle : 0.592 8.767 6614 Z= 0.296 Chirality : 0.042 0.195 755 Planarity : 0.004 0.039 816 Dihedral : 4.123 22.974 660 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.48 % Allowed : 20.12 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.62 (0.36), residues: 615 helix: 1.91 (0.31), residues: 335 sheet: 0.91 (0.51), residues: 122 loop : -0.57 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 136 HIS 0.001 0.000 HIS A 89 PHE 0.018 0.001 PHE A 341 TYR 0.021 0.002 TYR A 235 ARG 0.001 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.478 Fit side-chains REVERT: A 125 LYS cc_start: 0.6580 (mttt) cc_final: 0.6350 (mmtm) REVERT: A 176 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 308 MET cc_start: 0.6902 (mmt) cc_final: 0.6607 (tpp) REVERT: D 106 ASP cc_start: 0.7447 (m-30) cc_final: 0.6859 (m-30) REVERT: D 127 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7842 (tmmt) outliers start: 18 outliers final: 16 residues processed: 111 average time/residue: 0.1643 time to fit residues: 23.0729 Evaluate side-chains 116 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.7543 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4880 Z= 0.180 Angle : 0.604 8.655 6614 Z= 0.297 Chirality : 0.042 0.191 755 Planarity : 0.004 0.045 816 Dihedral : 4.091 22.956 660 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.48 % Allowed : 19.92 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.65 (0.36), residues: 615 helix: 1.94 (0.31), residues: 335 sheet: 0.86 (0.51), residues: 122 loop : -0.51 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 136 HIS 0.001 0.000 HIS A 155 PHE 0.018 0.001 PHE C 134 TYR 0.022 0.002 TYR A 235 ARG 0.002 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.533 Fit side-chains REVERT: A 125 LYS cc_start: 0.6703 (mttt) cc_final: 0.6376 (mmtm) REVERT: A 176 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8277 (mp) REVERT: A 308 MET cc_start: 0.6865 (mmt) cc_final: 0.6590 (tpp) REVERT: D 106 ASP cc_start: 0.7425 (m-30) cc_final: 0.6928 (m-30) REVERT: D 127 LYS cc_start: 0.8245 (ttpp) cc_final: 0.7802 (tmmt) outliers start: 18 outliers final: 16 residues processed: 111 average time/residue: 0.1680 time to fit residues: 23.8718 Evaluate side-chains 115 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7569 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4880 Z= 0.213 Angle : 0.625 8.941 6614 Z= 0.308 Chirality : 0.043 0.192 755 Planarity : 0.004 0.046 816 Dihedral : 4.095 22.855 660 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.87 % Allowed : 20.12 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.61 (0.36), residues: 615 helix: 1.90 (0.31), residues: 335 sheet: 0.77 (0.51), residues: 122 loop : -0.45 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 136 HIS 0.002 0.000 HIS A 155 PHE 0.024 0.001 PHE A 6 TYR 0.022 0.002 TYR A 235 ARG 0.002 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.479 Fit side-chains REVERT: A 125 LYS cc_start: 0.6775 (mttt) cc_final: 0.6431 (mmtm) REVERT: A 176 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8297 (mp) REVERT: A 308 MET cc_start: 0.6907 (mmt) cc_final: 0.6627 (tpp) REVERT: D 106 ASP cc_start: 0.7422 (m-30) cc_final: 0.6922 (m-30) REVERT: D 127 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7789 (tmmt) outliers start: 20 outliers final: 17 residues processed: 110 average time/residue: 0.1609 time to fit residues: 22.7669 Evaluate side-chains 114 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4880 Z= 0.203 Angle : 0.620 8.778 6614 Z= 0.306 Chirality : 0.043 0.191 755 Planarity : 0.004 0.048 816 Dihedral : 4.122 22.922 660 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.48 % Allowed : 20.70 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.57 (0.36), residues: 615 helix: 1.91 (0.31), residues: 335 sheet: 0.72 (0.51), residues: 122 loop : -0.51 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 136 HIS 0.002 0.000 HIS A 155 PHE 0.019 0.001 PHE C 134 TYR 0.024 0.002 TYR A 235 ARG 0.002 0.000 ARG C 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.507 Fit side-chains REVERT: A 125 LYS cc_start: 0.6869 (mttt) cc_final: 0.6515 (mmtm) REVERT: A 176 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8338 (mp) REVERT: A 308 MET cc_start: 0.6877 (mmt) cc_final: 0.6595 (tpp) REVERT: D 106 ASP cc_start: 0.7433 (m-30) cc_final: 0.6919 (m-30) REVERT: D 127 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7757 (tmmt) outliers start: 18 outliers final: 15 residues processed: 108 average time/residue: 0.1671 time to fit residues: 23.1486 Evaluate side-chains 112 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.180210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142595 restraints weight = 5668.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148340 restraints weight = 3293.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152274 restraints weight = 2344.606| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4880 Z= 0.181 Angle : 0.611 8.027 6614 Z= 0.299 Chirality : 0.042 0.188 755 Planarity : 0.004 0.048 816 Dihedral : 4.103 23.060 660 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.09 % Allowed : 21.28 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.65 (0.37), residues: 615 helix: 1.99 (0.31), residues: 335 sheet: 0.74 (0.51), residues: 122 loop : -0.52 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 136 HIS 0.001 0.000 HIS A 155 PHE 0.026 0.001 PHE A 6 TYR 0.025 0.001 TYR A 235 ARG 0.002 0.000 ARG C 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1320.55 seconds wall clock time: 24 minutes 7.54 seconds (1447.54 seconds total)