Starting phenix.real_space_refine on Thu Jul 18 23:39:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttf_41606/07_2024/8ttf_41606.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttf_41606/07_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_41606/07_2024/8ttf_41606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttf_41606/07_2024/8ttf_41606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttf_41606/07_2024/8ttf_41606.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttf_41606/07_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 3.16, per 1000 atoms: 0.66 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: 1.92 Conformation dependent library (CDL) restraints added in 860.9 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: 0.54 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: 1.39 Time building geometry restraints manager: 2.13 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 2.440 nonbonded pdb=" OG SER C 57 " pdb=" OE1 GLU C 128 " model vdw 2.270 2.440 nonbonded pdb=" OE1 GLN D 30 " pdb=" OG1 THR D 126 " model vdw 2.312 2.440 nonbonded pdb=" O SER A 81 " pdb=" OG SER A 97 " model vdw 2.328 2.440 nonbonded pdb=" NZ LYS A 68 " pdb=" O ILE A 177 " model vdw 2.335 2.520 ... (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 ========== 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.960 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 21.920 ------------------------------------------------------------------------------- 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 : 0.496 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: 0.1799 time to fit residues: 24.7749 Evaluate side-chains 97 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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: 3.9990 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4880 Z= 0.201 Angle : 0.603 11.357 6614 Z= 0.298 Chirality : 0.042 0.198 755 Planarity : 0.004 0.036 816 Dihedral : 4.227 22.297 660 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.16 % Allowed : 12.38 % Favored : 86.46 % 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: 1.50 (0.36), residues: 615 helix: 1.91 (0.31), residues: 327 sheet: 0.62 (0.50), residues: 122 loop : -0.49 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 136 HIS 0.003 0.001 HIS A 155 PHE 0.024 0.001 PHE C 134 TYR 0.020 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 110 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.503 Fit side-chains REVERT: A 231 ASP cc_start: 0.8273 (t70) cc_final: 0.7977 (t0) REVERT: A 308 MET cc_start: 0.6843 (mmt) cc_final: 0.6487 (tpp) REVERT: A 341 PHE cc_start: 0.7792 (t80) cc_final: 0.7278 (t80) REVERT: D 127 LYS cc_start: 0.8397 (ttpp) cc_final: 0.8057 (tmmt) outliers start: 6 outliers final: 4 residues processed: 106 average time/residue: 0.1657 time to fit residues: 22.4885 Evaluate side-chains 103 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain D residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 0.0670 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 GLN ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4880 Z= 0.161 Angle : 0.572 8.541 6614 Z= 0.280 Chirality : 0.041 0.201 755 Planarity : 0.004 0.031 816 Dihedral : 4.067 22.301 660 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.71 % Allowed : 14.31 % Favored : 82.98 % 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: 1.62 (0.36), residues: 615 helix: 2.02 (0.31), residues: 327 sheet: 0.62 (0.49), residues: 122 loop : -0.43 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 136 HIS 0.003 0.001 HIS C 61 PHE 0.022 0.001 PHE C 134 TYR 0.023 0.002 TYR A 235 ARG 0.002 0.000 ARG C 93 *********************** 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 110 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.555 Fit side-chains REVERT: A 308 MET cc_start: 0.6874 (mmt) cc_final: 0.6530 (tpp) REVERT: A 341 PHE cc_start: 0.7887 (t80) cc_final: 0.7663 (t80) REVERT: D 106 ASP cc_start: 0.7593 (m-30) cc_final: 0.7011 (m-30) REVERT: D 127 LYS cc_start: 0.8330 (ttpp) cc_final: 0.7952 (tmmt) outliers start: 14 outliers final: 7 residues processed: 102 average time/residue: 0.1690 time to fit residues: 22.1906 Evaluate side-chains 105 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 81 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.0050 chunk 57 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1375 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= 0.198 Angle : 0.585 8.738 6614 Z= 0.289 Chirality : 0.042 0.199 755 Planarity : 0.004 0.030 816 Dihedral : 4.063 22.420 660 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.29 % Allowed : 15.47 % Favored : 81.24 % 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: 1.98 (0.31), residues: 329 sheet: 0.59 (0.49), residues: 122 loop : -0.48 (0.49), residues: 164 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 0.014 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 122 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.488 Fit side-chains REVERT: A 231 ASP cc_start: 0.8238 (t70) cc_final: 0.7938 (t0) REVERT: A 308 MET cc_start: 0.6900 (mmt) cc_final: 0.6574 (tpp) REVERT: D 106 ASP cc_start: 0.7573 (m-30) cc_final: 0.7045 (m-30) REVERT: D 127 LYS cc_start: 0.8414 (ttpp) cc_final: 0.7999 (tmmt) outliers start: 17 outliers final: 12 residues processed: 112 average time/residue: 0.1530 time to fit residues: 22.2039 Evaluate side-chains 111 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 81 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 56 SER 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: 9.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1527 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= 0.168 Angle : 0.564 8.346 6614 Z= 0.280 Chirality : 0.042 0.193 755 Planarity : 0.004 0.030 816 Dihedral : 4.016 22.706 660 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.09 % Allowed : 18.18 % Favored : 78.72 % 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: 2.03 (0.30), residues: 329 sheet: 0.63 (0.50), residues: 122 loop : -0.52 (0.48), residues: 164 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 0.016 0.001 PHE C 134 TYR 0.019 0.001 TYR A 235 ARG 0.001 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 118 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.500 Fit side-chains REVERT: A 308 MET cc_start: 0.6888 (mmt) cc_final: 0.6567 (tpp) REVERT: D 106 ASP cc_start: 0.7571 (m-30) cc_final: 0.7046 (m-30) REVERT: D 127 LYS cc_start: 0.8387 (ttpp) cc_final: 0.7962 (tmmt) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 0.1640 time to fit residues: 23.3720 Evaluate side-chains 110 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 81 SER Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 283 LEU 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 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: 4.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 chunk 30 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4880 Z= 0.220 Angle : 0.591 7.826 6614 Z= 0.299 Chirality : 0.042 0.194 755 Planarity : 0.004 0.039 816 Dihedral : 4.044 22.656 660 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.48 % Allowed : 18.38 % Favored : 78.14 % 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: 1.59 (0.36), residues: 615 helix: 2.00 (0.31), residues: 329 sheet: 0.59 (0.50), residues: 122 loop : -0.48 (0.49), 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 0.018 0.001 PHE C 134 TYR 0.017 0.002 TYR C 133 ARG 0.002 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 126 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.501 Fit side-chains REVERT: A 308 MET cc_start: 0.6899 (mmt) cc_final: 0.6600 (tpp) REVERT: D 106 ASP cc_start: 0.7662 (m-30) cc_final: 0.7136 (m-30) REVERT: D 127 LYS cc_start: 0.8425 (ttpp) cc_final: 0.7991 (tmmt) outliers start: 18 outliers final: 15 residues processed: 118 average time/residue: 0.1612 time to fit residues: 24.4760 Evaluate side-chains 118 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 81 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 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 135 TYR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 98 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: 1.9990 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 39 optimal weight: 10.0000 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1749 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= 0.185 Angle : 0.583 7.339 6614 Z= 0.291 Chirality : 0.041 0.192 755 Planarity : 0.004 0.042 816 Dihedral : 3.981 22.809 660 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.87 % Allowed : 18.18 % Favored : 77.95 % 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: 2.06 (0.31), residues: 329 sheet: 0.58 (0.50), residues: 122 loop : -0.47 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 136 HIS 0.001 0.000 HIS A 155 PHE 0.020 0.001 PHE A 6 TYR 0.021 0.001 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 120 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.528 Fit side-chains REVERT: A 176 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 308 MET cc_start: 0.6908 (mmt) cc_final: 0.6591 (tpp) REVERT: D 106 ASP cc_start: 0.7665 (m-30) cc_final: 0.7144 (m-30) REVERT: D 127 LYS cc_start: 0.8403 (ttpp) cc_final: 0.7984 (tmmt) outliers start: 20 outliers final: 15 residues processed: 112 average time/residue: 0.1534 time to fit residues: 22.4878 Evaluate side-chains 116 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 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 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 125 MET Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4880 Z= 0.194 Angle : 0.592 8.695 6614 Z= 0.294 Chirality : 0.041 0.192 755 Planarity : 0.004 0.042 816 Dihedral : 3.981 22.740 660 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.68 % Allowed : 18.76 % Favored : 77.56 % 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: 1.58 (0.36), residues: 615 helix: 2.00 (0.31), residues: 329 sheet: 0.58 (0.50), residues: 122 loop : -0.49 (0.50), residues: 164 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 0.018 0.001 PHE C 134 TYR 0.020 0.001 TYR A 235 ARG 0.001 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: 19 poor density : 99 time to evaluate : 0.550 Fit side-chains REVERT: A 176 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8311 (mp) REVERT: A 308 MET cc_start: 0.6911 (mmt) cc_final: 0.6601 (tpp) REVERT: D 106 ASP cc_start: 0.7651 (m-30) cc_final: 0.7146 (m-30) REVERT: D 127 LYS cc_start: 0.8443 (ttpp) cc_final: 0.7994 (tmmt) outliers start: 19 outliers final: 16 residues processed: 111 average time/residue: 0.1584 time to fit residues: 23.1956 Evaluate side-chains 114 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 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 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 C residue 151 LEU Chi-restraints excluded: chain D residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 0.0040 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.0570 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4880 Z= 0.164 Angle : 0.597 8.526 6614 Z= 0.289 Chirality : 0.041 0.187 755 Planarity : 0.004 0.042 816 Dihedral : 3.956 22.860 660 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.32 % Allowed : 20.89 % Favored : 76.79 % 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: 1.68 (0.37), residues: 615 helix: 2.15 (0.31), residues: 329 sheet: 0.60 (0.50), residues: 122 loop : -0.58 (0.50), residues: 164 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 0.024 0.001 PHE A 6 TYR 0.020 0.001 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 110 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.456 Fit side-chains REVERT: A 176 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8334 (mp) REVERT: A 308 MET cc_start: 0.6864 (mmt) cc_final: 0.6575 (tpp) REVERT: C 44 LEU cc_start: 0.7333 (tp) cc_final: 0.7126 (tt) REVERT: D 106 ASP cc_start: 0.7569 (m-30) cc_final: 0.7066 (m-30) REVERT: D 127 LYS cc_start: 0.8371 (ttpp) cc_final: 0.7919 (tmmt) outliers start: 12 outliers final: 11 residues processed: 105 average time/residue: 0.1564 time to fit residues: 21.5544 Evaluate side-chains 110 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 283 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.0170 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1947 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= 0.185 Angle : 0.600 8.491 6614 Z= 0.293 Chirality : 0.041 0.189 755 Planarity : 0.004 0.044 816 Dihedral : 3.950 22.613 660 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.51 % Allowed : 20.31 % Favored : 77.18 % 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: 1.66 (0.36), residues: 615 helix: 2.12 (0.31), residues: 329 sheet: 0.58 (0.50), residues: 122 loop : -0.55 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 136 HIS 0.001 0.000 HIS A 155 PHE 0.018 0.001 PHE C 134 TYR 0.024 0.001 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 112 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.510 Fit side-chains REVERT: A 176 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8363 (mp) REVERT: A 308 MET cc_start: 0.6971 (mmt) cc_final: 0.6673 (tpp) REVERT: C 44 LEU cc_start: 0.7344 (tp) cc_final: 0.7120 (tt) REVERT: D 106 ASP cc_start: 0.7513 (m-30) cc_final: 0.6947 (m-30) REVERT: D 127 LYS cc_start: 0.8376 (ttpp) cc_final: 0.7912 (tmmt) outliers start: 13 outliers final: 12 residues processed: 107 average time/residue: 0.1623 time to fit residues: 22.1838 Evaluate side-chains 112 residues out of total 517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 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 283 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.0020 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.180708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143496 restraints weight = 5670.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149243 restraints weight = 3250.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153048 restraints weight = 2303.066| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4880 Z= 0.184 Angle : 0.594 8.128 6614 Z= 0.290 Chirality : 0.041 0.188 755 Planarity : 0.004 0.047 816 Dihedral : 3.927 22.659 660 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.71 % Allowed : 20.31 % 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: 1.71 (0.37), residues: 615 helix: 2.16 (0.31), residues: 329 sheet: 0.63 (0.51), residues: 122 loop : -0.58 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 136 HIS 0.001 0.000 HIS A 155 PHE 0.025 0.001 PHE A 6 TYR 0.018 0.001 TYR A 235 ARG 0.002 0.000 ARG D 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1348.83 seconds wall clock time: 24 minutes 38.59 seconds (1478.59 seconds total)