Starting phenix.real_space_refine on Thu Mar 6 03:33:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ttf_41606/03_2025/8ttf_41606.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ttf_41606/03_2025/8ttf_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/cci-nas-00/data/ceres_data/8ttf_41606/03_2025/8ttf_41606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ttf_41606/03_2025/8ttf_41606.map" model { file = "/net/cci-nas-00/data/ceres_data/8ttf_41606/03_2025/8ttf_41606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ttf_41606/03_2025/8ttf_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. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.49, per 1000 atoms: 0.73 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 - 3.00 Amino acid : True - 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: 1.25 Conformation dependent library (CDL) restraints added in 621.1 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: 0.47 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: 1.30 Time building geometry restraints manager: 1.49 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: 0.00 - 1.74: 6488 1.74 - 3.49: 95 3.49 - 5.23: 24 5.23 - 6.98: 6 6.98 - 8.72: 1 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: 1.220 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.840 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.470 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.482 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: 0.1825 time to fit residues: 25.3737 Evaluate side-chains 97 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.187162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149953 restraints weight = 5568.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155695 restraints weight = 3317.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.159557 restraints weight = 2397.249| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 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 to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.889 Fit side-chains REVERT: A 231 ASP cc_start: 0.8336 (t70) cc_final: 0.8043 (t0) REVERT: A 308 MET cc_start: 0.6876 (mmt) cc_final: 0.6520 (tpp) REVERT: A 341 PHE cc_start: 0.7720 (t80) cc_final: 0.7200 (t80) REVERT: D 127 LYS cc_start: 0.8411 (ttpp) cc_final: 0.8047 (tmmt) outliers start: 6 outliers final: 2 residues processed: 105 average time/residue: 0.1714 time to fit residues: 23.1783 Evaluate side-chains 97 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 0.0470 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.182084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145260 restraints weight = 5635.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151161 restraints weight = 3180.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155197 restraints weight = 2223.486| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4880 Z= 0.148 Angle : 0.574 8.721 6614 Z= 0.282 Chirality : 0.041 0.196 755 Planarity : 0.004 0.032 816 Dihedral : 4.072 22.184 660 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.51 % Allowed : 14.12 % Favored : 83.37 % 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: 1.70 (0.36), residues: 615 helix: 2.07 (0.31), residues: 327 sheet: 0.68 (0.50), residues: 122 loop : -0.38 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 136 HIS 0.003 0.001 HIS C 61 PHE 0.017 0.001 PHE A 341 TYR 0.020 0.001 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 113 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.538 Fit side-chains REVERT: A 308 MET cc_start: 0.6838 (mmt) cc_final: 0.6483 (tpp) REVERT: A 341 PHE cc_start: 0.7752 (t80) cc_final: 0.7501 (t80) REVERT: D 127 LYS cc_start: 0.8404 (ttpp) cc_final: 0.7999 (tmmt) outliers start: 13 outliers final: 5 residues processed: 105 average time/residue: 0.1575 time to fit residues: 21.4269 Evaluate side-chains 101 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 285 LEU 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 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.175256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138001 restraints weight = 5742.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143438 restraints weight = 3338.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147157 restraints weight = 2377.867| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4880 Z= 0.284 Angle : 0.643 8.909 6614 Z= 0.324 Chirality : 0.045 0.200 755 Planarity : 0.004 0.033 816 Dihedral : 4.222 22.380 660 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.29 % Allowed : 17.02 % Favored : 79.69 % 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: 1.33 (0.36), residues: 615 helix: 1.68 (0.30), residues: 329 sheet: 0.67 (0.50), residues: 122 loop : -0.50 (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 89 PHE 0.018 0.002 PHE C 134 TYR 0.021 0.002 TYR A 235 ARG 0.003 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 126 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.536 Fit side-chains REVERT: A 125 LYS cc_start: 0.6690 (mttt) cc_final: 0.6405 (mmtm) REVERT: A 231 ASP cc_start: 0.8410 (t70) cc_final: 0.8158 (t0) REVERT: A 308 MET cc_start: 0.7049 (mmt) cc_final: 0.6750 (tpp) REVERT: D 127 LYS cc_start: 0.8397 (ttpp) cc_final: 0.7968 (tmmt) outliers start: 17 outliers final: 11 residues processed: 117 average time/residue: 0.1795 time to fit residues: 26.6103 Evaluate side-chains 114 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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 117 THR Chi-restraints excluded: chain C residue 151 LEU 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 55 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.181459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143698 restraints weight = 5626.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149648 restraints weight = 3235.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.153641 restraints weight = 2275.073| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4880 Z= 0.185 Angle : 0.593 8.864 6614 Z= 0.294 Chirality : 0.042 0.196 755 Planarity : 0.004 0.033 816 Dihedral : 4.130 22.939 660 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.09 % Allowed : 18.57 % Favored : 78.34 % 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: 1.94 (0.31), residues: 329 sheet: 0.77 (0.50), residues: 122 loop : -0.54 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 136 HIS 0.002 0.000 HIS A 155 PHE 0.017 0.001 PHE C 134 TYR 0.021 0.002 TYR A 235 ARG 0.003 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 117 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.507 Fit side-chains REVERT: A 125 LYS cc_start: 0.6710 (mttt) cc_final: 0.6392 (mmtm) REVERT: A 308 MET cc_start: 0.6978 (mmt) cc_final: 0.6688 (tpp) REVERT: D 127 LYS cc_start: 0.8361 (ttpp) cc_final: 0.7908 (tmmt) outliers start: 16 outliers final: 14 residues processed: 109 average time/residue: 0.1702 time to fit residues: 23.6966 Evaluate side-chains 114 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 133 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.0020 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.179712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141159 restraints weight = 5638.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.147098 restraints weight = 3273.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151115 restraints weight = 2321.553| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4880 Z= 0.165 Angle : 0.567 8.674 6614 Z= 0.285 Chirality : 0.041 0.191 755 Planarity : 0.004 0.034 816 Dihedral : 4.037 22.975 660 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.68 % Allowed : 18.96 % Favored : 77.37 % 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: 1.75 (0.36), residues: 615 helix: 2.10 (0.31), residues: 329 sheet: 0.83 (0.51), residues: 122 loop : -0.49 (0.49), residues: 164 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 0.017 0.001 PHE C 134 TYR 0.020 0.002 TYR A 235 ARG 0.002 0.000 ARG D 85 *********************** 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 119 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.518 Fit side-chains REVERT: A 308 MET cc_start: 0.6980 (mmt) cc_final: 0.6698 (tpp) REVERT: C 44 LEU cc_start: 0.7665 (tp) cc_final: 0.7463 (tt) REVERT: D 28 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7645 (tpp) REVERT: D 127 LYS cc_start: 0.8326 (ttpp) cc_final: 0.7856 (tmmt) outliers start: 19 outliers final: 13 residues processed: 110 average time/residue: 0.1607 time to fit residues: 22.7087 Evaluate side-chains 113 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 133 SER 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 100 THR 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 28 MET 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 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.181069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142872 restraints weight = 5671.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148810 restraints weight = 3314.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152904 restraints weight = 2360.724| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1787 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= 0.189 Angle : 0.587 8.888 6614 Z= 0.293 Chirality : 0.042 0.192 755 Planarity : 0.004 0.033 816 Dihedral : 4.023 22.844 660 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.26 % Allowed : 19.73 % 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: 1.79 (0.36), residues: 615 helix: 2.12 (0.31), residues: 329 sheet: 0.87 (0.51), residues: 122 loop : -0.46 (0.49), 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 0.002 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 125 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.531 Fit side-chains REVERT: A 125 LYS cc_start: 0.6694 (mttt) cc_final: 0.6342 (mmtm) REVERT: A 176 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 308 MET cc_start: 0.6970 (mmt) cc_final: 0.6693 (tpp) REVERT: D 106 ASP cc_start: 0.7777 (m-30) cc_final: 0.7445 (m-30) REVERT: D 127 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7810 (tmmt) outliers start: 22 outliers final: 16 residues processed: 115 average time/residue: 0.1684 time to fit residues: 24.8786 Evaluate side-chains 117 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.178929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141552 restraints weight = 5750.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147255 restraints weight = 3308.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151213 restraints weight = 2337.782| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.003 0.039 4880 Z= 0.201 Angle : 0.632 8.941 6614 Z= 0.306 Chirality : 0.042 0.191 755 Planarity : 0.004 0.036 816 Dihedral : 4.053 22.867 660 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.06 % Allowed : 20.89 % Favored : 75.05 % 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: 1.74 (0.36), residues: 615 helix: 2.07 (0.31), residues: 329 sheet: 0.84 (0.52), residues: 122 loop : -0.45 (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 0.021 0.001 PHE A 6 TYR 0.020 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 120 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.514 Fit side-chains REVERT: A 125 LYS cc_start: 0.6709 (mttt) cc_final: 0.6315 (mmtm) REVERT: A 176 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 308 MET cc_start: 0.6981 (mmt) cc_final: 0.6712 (tpp) REVERT: D 106 ASP cc_start: 0.7666 (m-30) cc_final: 0.7336 (m-30) REVERT: D 127 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7780 (tmmt) outliers start: 21 outliers final: 16 residues processed: 113 average time/residue: 0.1618 time to fit residues: 23.4812 Evaluate side-chains 116 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 3 optimal weight: 0.0030 chunk 49 optimal weight: 0.0050 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.0030 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.3014 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.181821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144552 restraints weight = 5720.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.150461 restraints weight = 3268.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154324 restraints weight = 2300.453| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4880 Z= 0.153 Angle : 0.588 8.529 6614 Z= 0.289 Chirality : 0.042 0.185 755 Planarity : 0.004 0.040 816 Dihedral : 4.003 22.992 660 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.51 % Allowed : 21.47 % 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: 1.76 (0.37), residues: 615 helix: 2.09 (0.31), residues: 335 sheet: 0.83 (0.51), residues: 122 loop : -0.56 (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 0.017 0.001 PHE C 134 TYR 0.021 0.001 TYR A 235 ARG 0.001 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 109 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.496 Fit side-chains REVERT: A 176 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 308 MET cc_start: 0.6869 (mmt) cc_final: 0.6421 (tpp) REVERT: D 106 ASP cc_start: 0.7647 (m-30) cc_final: 0.7357 (m-30) REVERT: D 127 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7758 (tmmt) outliers start: 13 outliers final: 10 residues processed: 103 average time/residue: 0.1710 time to fit residues: 22.4594 Evaluate side-chains 107 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.179040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.140818 restraints weight = 5689.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146579 restraints weight = 3352.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150492 restraints weight = 2405.957| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4880 Z= 0.220 Angle : 0.649 14.040 6614 Z= 0.313 Chirality : 0.044 0.352 755 Planarity : 0.004 0.044 816 Dihedral : 4.060 22.576 660 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.93 % Allowed : 21.66 % 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: 1.73 (0.36), residues: 615 helix: 2.06 (0.31), residues: 329 sheet: 0.83 (0.51), residues: 122 loop : -0.45 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 136 HIS 0.002 0.000 HIS A 155 PHE 0.025 0.002 PHE A 6 TYR 0.021 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 111 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.557 Fit side-chains REVERT: A 125 LYS cc_start: 0.6937 (mttt) cc_final: 0.6385 (mmtm) REVERT: A 308 MET cc_start: 0.6960 (mmt) cc_final: 0.6691 (tpp) REVERT: C 143 MET cc_start: 0.7971 (mtt) cc_final: 0.7582 (mtt) REVERT: D 127 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7735 (tmmt) outliers start: 10 outliers final: 10 residues processed: 108 average time/residue: 0.1710 time to fit residues: 23.6633 Evaluate side-chains 111 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 174 ILE 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 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 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.178245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140551 restraints weight = 5740.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146330 restraints weight = 3313.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150207 restraints weight = 2350.979| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4880 Z= 0.210 Angle : 0.640 11.002 6614 Z= 0.310 Chirality : 0.044 0.325 755 Planarity : 0.004 0.042 816 Dihedral : 4.103 22.898 660 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.51 % Allowed : 21.28 % Favored : 76.21 % 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: 2.06 (0.31), residues: 329 sheet: 0.76 (0.51), residues: 122 loop : -0.49 (0.50), 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 0.023 0.002 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: 1801.02 seconds wall clock time: 31 minutes 56.04 seconds (1916.04 seconds total)