Starting phenix.real_space_refine on Mon Apr 28 10:52:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ofz_16864/04_2025/8ofz_16864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ofz_16864/04_2025/8ofz_16864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ofz_16864/04_2025/8ofz_16864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ofz_16864/04_2025/8ofz_16864.map" model { file = "/net/cci-nas-00/data/ceres_data/8ofz_16864/04_2025/8ofz_16864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ofz_16864/04_2025/8ofz_16864.cif" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= -0.015 sd= 0.441 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 32 5.16 5 C 4952 2.51 5 N 1124 2.21 5 O 1260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7368 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1830 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 230} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {'GOL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, D Time building chain proxies: 3.50, per 1000 atoms: 0.48 Number of scatterers: 7368 At special positions: 0 Unit cell: (82.39, 82.39, 67.41, 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 32 16.00 O 1260 8.00 N 1124 7.00 C 4952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 77.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 71 through 98 Processing helix chain 'A' and resid 102 through 122 Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 146 through 178 removed outlier: 4.255A pdb=" N GLY A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.062A pdb=" N PHE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 227 Processing helix chain 'A' and resid 236 through 256 removed outlier: 3.954A pdb=" N LEU A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.518A pdb=" N ASP A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 288 through 310 Proline residue: A 295 - end of helix Processing helix chain 'B' and resid 71 through 98 Processing helix chain 'B' and resid 102 through 122 Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 146 through 178 removed outlier: 4.255A pdb=" N GLY B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 removed outlier: 4.062A pdb=" N PHE B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 227 Processing helix chain 'B' and resid 236 through 256 removed outlier: 3.954A pdb=" N LEU B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 276 removed outlier: 3.518A pdb=" N ASP B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 288 through 310 Proline residue: B 295 - end of helix Processing helix chain 'C' and resid 71 through 98 Processing helix chain 'C' and resid 102 through 122 Processing helix chain 'C' and resid 130 through 140 Processing helix chain 'C' and resid 146 through 178 removed outlier: 4.255A pdb=" N GLY C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU C 173 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.062A pdb=" N PHE C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 227 Processing helix chain 'C' and resid 236 through 256 removed outlier: 3.954A pdb=" N LEU C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 276 removed outlier: 3.518A pdb=" N ASP C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) Proline residue: C 268 - end of helix Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 288 through 310 Proline residue: C 295 - end of helix Processing helix chain 'D' and resid 71 through 98 Processing helix chain 'D' and resid 102 through 122 Processing helix chain 'D' and resid 130 through 140 Processing helix chain 'D' and resid 146 through 178 removed outlier: 4.255A pdb=" N GLY D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU D 173 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 removed outlier: 4.062A pdb=" N PHE D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 227 Processing helix chain 'D' and resid 236 through 256 removed outlier: 3.954A pdb=" N LEU D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 276 removed outlier: 3.518A pdb=" N ASP D 265 " --> pdb=" O ASN D 261 " (cutoff:3.500A) Proline residue: D 268 - end of helix Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 288 through 310 Proline residue: D 295 - end of helix 544 hydrogen bonds defined for protein. 1632 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: 2.10 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1260 1.34 - 1.46: 2228 1.46 - 1.58: 4048 1.58 - 1.70: 0 1.70 - 1.82: 52 Bond restraints: 7588 Sorted by residual: bond pdb=" C PHE A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.332 1.367 -0.036 1.30e-02 5.92e+03 7.48e+00 bond pdb=" C PHE D 143 " pdb=" N PRO D 144 " ideal model delta sigma weight residual 1.332 1.367 -0.036 1.30e-02 5.92e+03 7.48e+00 bond pdb=" C PHE B 143 " pdb=" N PRO B 144 " ideal model delta sigma weight residual 1.332 1.367 -0.036 1.30e-02 5.92e+03 7.48e+00 bond pdb=" C PHE C 143 " pdb=" N PRO C 144 " ideal model delta sigma weight residual 1.332 1.367 -0.036 1.30e-02 5.92e+03 7.48e+00 bond pdb=" C VAL D 290 " pdb=" N PRO D 291 " ideal model delta sigma weight residual 1.335 1.366 -0.032 1.19e-02 7.06e+03 7.15e+00 ... (remaining 7583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 7308 1.71 - 3.42: 2536 3.42 - 5.13: 364 5.13 - 6.84: 112 6.84 - 8.55: 28 Bond angle restraints: 10348 Sorted by residual: angle pdb=" CA ASN D 202 " pdb=" CB ASN D 202 " pdb=" CG ASN D 202 " ideal model delta sigma weight residual 112.60 118.75 -6.15 1.00e+00 1.00e+00 3.78e+01 angle pdb=" CA ASN A 202 " pdb=" CB ASN A 202 " pdb=" CG ASN A 202 " ideal model delta sigma weight residual 112.60 118.75 -6.15 1.00e+00 1.00e+00 3.78e+01 angle pdb=" CA ASN C 202 " pdb=" CB ASN C 202 " pdb=" CG ASN C 202 " ideal model delta sigma weight residual 112.60 118.75 -6.15 1.00e+00 1.00e+00 3.78e+01 angle pdb=" CA ASN B 202 " pdb=" CB ASN B 202 " pdb=" CG ASN B 202 " ideal model delta sigma weight residual 112.60 118.75 -6.15 1.00e+00 1.00e+00 3.78e+01 angle pdb=" C PRO D 291 " pdb=" CA PRO D 291 " pdb=" CB PRO D 291 " ideal model delta sigma weight residual 111.85 104.63 7.22 1.42e+00 4.96e-01 2.59e+01 ... (remaining 10343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 3632 14.11 - 28.21: 416 28.21 - 42.31: 76 42.31 - 56.42: 60 56.42 - 70.52: 16 Dihedral angle restraints: 4200 sinusoidal: 1480 harmonic: 2720 Sorted by residual: dihedral pdb=" CA SER A 125 " pdb=" C SER A 125 " pdb=" N GLY A 126 " pdb=" CA GLY A 126 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA SER B 125 " pdb=" C SER B 125 " pdb=" N GLY B 126 " pdb=" CA GLY B 126 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA SER C 125 " pdb=" C SER C 125 " pdb=" N GLY C 126 " pdb=" CA GLY C 126 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 588 0.044 - 0.089: 320 0.089 - 0.133: 168 0.133 - 0.177: 64 0.177 - 0.221: 16 Chirality restraints: 1156 Sorted by residual: chirality pdb=" CA HIS A 312 " pdb=" N HIS A 312 " pdb=" C HIS A 312 " pdb=" CB HIS A 312 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA HIS D 312 " pdb=" N HIS D 312 " pdb=" C HIS D 312 " pdb=" CB HIS D 312 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA HIS C 312 " pdb=" N HIS C 312 " pdb=" C HIS C 312 " pdb=" CB HIS C 312 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1153 not shown) Planarity restraints: 1300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 246 " -0.053 2.00e-02 2.50e+03 3.67e-02 2.36e+01 pdb=" CG PHE C 246 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE C 246 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 246 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE C 246 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 246 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE C 246 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 246 " -0.053 2.00e-02 2.50e+03 3.67e-02 2.36e+01 pdb=" CG PHE D 246 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE D 246 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 246 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE D 246 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 246 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE D 246 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 246 " 0.053 2.00e-02 2.50e+03 3.67e-02 2.36e+01 pdb=" CG PHE B 246 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE B 246 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 246 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE B 246 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 246 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE B 246 " 0.011 2.00e-02 2.50e+03 ... (remaining 1297 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1476 2.83 - 3.35: 7988 3.35 - 3.87: 14156 3.87 - 4.38: 16436 4.38 - 4.90: 27130 Nonbonded interactions: 67186 Sorted by model distance: nonbonded pdb=" OG1 THR B 94 " pdb=" O ASN C 251 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR A 94 " pdb=" O ASN B 251 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR C 94 " pdb=" O ASN D 251 " model vdw 2.314 3.040 nonbonded pdb=" O ASN A 251 " pdb=" OG1 THR D 94 " model vdw 2.314 3.040 nonbonded pdb=" OG SER A 131 " pdb=" OG SER A 263 " model vdw 2.560 3.040 ... (remaining 67181 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.380 Find NCS groups from input model: 0.150 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 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 : 0.010 0.046 7588 Z= 0.650 Angle : 1.740 8.545 10348 Z= 1.227 Chirality : 0.070 0.221 1156 Planarity : 0.014 0.150 1300 Dihedral : 14.614 70.519 2504 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.52 % Allowed : 5.52 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.23), residues: 968 helix: -0.34 (0.17), residues: 652 sheet: None (None), residues: 0 loop : -1.90 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP C 192 HIS 0.010 0.003 HIS C 177 PHE 0.070 0.009 PHE C 246 TYR 0.040 0.009 TYR C 206 ARG 0.013 0.005 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.17003 ( 544) hydrogen bonds : angle 7.64525 ( 1632) covalent geometry : bond 0.00971 ( 7588) covalent geometry : angle 1.74031 (10348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.763 Fit side-chains REVERT: A 77 GLU cc_start: 0.7608 (tp30) cc_final: 0.6884 (tp30) REVERT: A 146 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6008 (mmp80) REVERT: A 175 LYS cc_start: 0.5305 (OUTLIER) cc_final: 0.4934 (mttp) REVERT: A 177 HIS cc_start: 0.6632 (t70) cc_final: 0.6418 (t-90) REVERT: B 77 GLU cc_start: 0.7608 (tp30) cc_final: 0.6885 (tp30) REVERT: B 146 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6007 (mmp80) REVERT: B 175 LYS cc_start: 0.5304 (OUTLIER) cc_final: 0.4934 (mttp) REVERT: B 177 HIS cc_start: 0.6631 (t70) cc_final: 0.6417 (t-90) REVERT: C 77 GLU cc_start: 0.7607 (tp30) cc_final: 0.6884 (tp30) REVERT: C 146 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6008 (mmp80) REVERT: C 175 LYS cc_start: 0.5305 (OUTLIER) cc_final: 0.4935 (mttp) REVERT: C 177 HIS cc_start: 0.6632 (t70) cc_final: 0.6418 (t-90) REVERT: D 77 GLU cc_start: 0.7608 (tp30) cc_final: 0.6884 (tp30) REVERT: D 146 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6008 (mmp80) REVERT: D 175 LYS cc_start: 0.5304 (OUTLIER) cc_final: 0.4934 (mttp) REVERT: D 177 HIS cc_start: 0.6632 (t70) cc_final: 0.6417 (t-90) outliers start: 40 outliers final: 8 residues processed: 184 average time/residue: 0.1989 time to fit residues: 49.4418 Evaluate side-chains 148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 312 HIS Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 229 ASN Chi-restraints excluded: chain D residue 312 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 137 ASN B 81 ASN B 137 ASN C 81 ASN C 137 ASN D 81 ASN D 137 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.128895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.111976 restraints weight = 8152.869| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.49 r_work: 0.2981 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7588 Z= 0.146 Angle : 0.613 5.685 10348 Z= 0.324 Chirality : 0.040 0.121 1156 Planarity : 0.005 0.034 1300 Dihedral : 7.862 58.059 1104 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.10 % Allowed : 9.94 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 968 helix: 1.67 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.79 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 289 HIS 0.001 0.001 HIS B 283 PHE 0.018 0.002 PHE D 140 TYR 0.015 0.002 TYR C 206 ARG 0.002 0.001 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 544) hydrogen bonds : angle 5.11833 ( 1632) covalent geometry : bond 0.00318 ( 7588) covalent geometry : angle 0.61313 (10348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.690 Fit side-chains REVERT: A 146 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6971 (mmp-170) REVERT: A 175 LYS cc_start: 0.7685 (tttt) cc_final: 0.7085 (mttp) REVERT: A 177 HIS cc_start: 0.8015 (t70) cc_final: 0.7760 (t-90) REVERT: B 146 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6973 (mmp-170) REVERT: B 175 LYS cc_start: 0.7686 (tttt) cc_final: 0.7090 (mttp) REVERT: B 177 HIS cc_start: 0.8023 (t70) cc_final: 0.7763 (t-90) REVERT: C 146 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6971 (mmp-170) REVERT: C 175 LYS cc_start: 0.7680 (tttt) cc_final: 0.7091 (mttp) REVERT: C 177 HIS cc_start: 0.8017 (t70) cc_final: 0.7756 (t-90) REVERT: D 146 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6967 (mmp-170) REVERT: D 175 LYS cc_start: 0.7699 (tttt) cc_final: 0.7099 (mttp) REVERT: D 177 HIS cc_start: 0.8023 (t70) cc_final: 0.7769 (t-90) outliers start: 8 outliers final: 4 residues processed: 180 average time/residue: 0.1744 time to fit residues: 43.2013 Evaluate side-chains 176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 312 HIS Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 312 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 0.0060 chunk 79 optimal weight: 0.0470 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.4894 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.132497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.115886 restraints weight = 8255.807| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.50 r_work: 0.3028 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7588 Z= 0.122 Angle : 0.568 5.781 10348 Z= 0.298 Chirality : 0.039 0.116 1156 Planarity : 0.005 0.038 1300 Dihedral : 6.859 49.173 1080 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.10 % Allowed : 10.50 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 968 helix: 1.97 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.89 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 289 HIS 0.002 0.001 HIS C 177 PHE 0.014 0.001 PHE A 140 TYR 0.011 0.001 TYR D 206 ARG 0.002 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 544) hydrogen bonds : angle 4.72903 ( 1632) covalent geometry : bond 0.00256 ( 7588) covalent geometry : angle 0.56840 (10348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.709 Fit side-chains REVERT: A 146 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6882 (mmp-170) REVERT: A 147 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7751 (mmtm) REVERT: A 175 LYS cc_start: 0.7626 (tttt) cc_final: 0.7263 (mttp) REVERT: B 146 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6887 (mmp-170) REVERT: B 147 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7753 (mmtm) REVERT: B 175 LYS cc_start: 0.7616 (tttt) cc_final: 0.7249 (mttp) REVERT: C 146 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6881 (mmp-170) REVERT: C 147 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7740 (mmtm) REVERT: C 175 LYS cc_start: 0.7617 (tttt) cc_final: 0.7264 (mttp) REVERT: D 146 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6880 (mmp-170) REVERT: D 147 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7749 (mmtm) REVERT: D 175 LYS cc_start: 0.7614 (tttt) cc_final: 0.7261 (mttp) outliers start: 8 outliers final: 4 residues processed: 176 average time/residue: 0.1871 time to fit residues: 44.3371 Evaluate side-chains 168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 312 HIS Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 312 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 0.0470 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 HIS ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.129708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.112732 restraints weight = 8269.658| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.52 r_work: 0.2974 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7588 Z= 0.133 Angle : 0.602 8.459 10348 Z= 0.296 Chirality : 0.039 0.122 1156 Planarity : 0.005 0.041 1300 Dihedral : 6.587 45.754 1080 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.76 % Allowed : 11.60 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 968 helix: 1.94 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.89 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 289 HIS 0.006 0.001 HIS A 177 PHE 0.015 0.002 PHE A 140 TYR 0.012 0.001 TYR D 306 ARG 0.001 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 544) hydrogen bonds : angle 4.72431 ( 1632) covalent geometry : bond 0.00292 ( 7588) covalent geometry : angle 0.60194 (10348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.704 Fit side-chains REVERT: A 146 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7034 (mmp-170) REVERT: A 147 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7775 (mttt) REVERT: A 175 LYS cc_start: 0.7506 (tttt) cc_final: 0.7258 (mttp) REVERT: B 146 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7040 (mmp-170) REVERT: B 147 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7769 (mttt) REVERT: B 175 LYS cc_start: 0.7510 (tttt) cc_final: 0.7267 (mttp) REVERT: C 146 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7033 (mmp-170) REVERT: C 147 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7767 (mttt) REVERT: C 175 LYS cc_start: 0.7514 (tttt) cc_final: 0.7266 (mttp) REVERT: D 146 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7033 (mmp-170) REVERT: D 147 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7776 (mttt) REVERT: D 175 LYS cc_start: 0.7510 (tttt) cc_final: 0.7258 (mttp) outliers start: 20 outliers final: 4 residues processed: 180 average time/residue: 0.1816 time to fit residues: 44.2898 Evaluate side-chains 156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 261 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 9.9990 chunk 42 optimal weight: 0.0970 chunk 72 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 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 = 0.3222 r_free = 0.3222 target = 0.123600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.106143 restraints weight = 8359.373| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.51 r_work: 0.2894 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7588 Z= 0.183 Angle : 0.643 7.486 10348 Z= 0.320 Chirality : 0.041 0.132 1156 Planarity : 0.005 0.044 1300 Dihedral : 6.043 48.373 1072 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.31 % Allowed : 13.81 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 968 helix: 1.76 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.82 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 192 HIS 0.001 0.000 HIS B 128 PHE 0.019 0.002 PHE C 246 TYR 0.021 0.002 TYR B 306 ARG 0.001 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 544) hydrogen bonds : angle 4.95673 ( 1632) covalent geometry : bond 0.00423 ( 7588) covalent geometry : angle 0.64323 (10348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7002 (mmp-170) REVERT: A 175 LYS cc_start: 0.7551 (tttt) cc_final: 0.7297 (mttp) REVERT: B 146 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.6998 (mmp-170) REVERT: B 175 LYS cc_start: 0.7551 (tttt) cc_final: 0.7289 (mttp) REVERT: C 146 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6992 (mmp-170) REVERT: C 175 LYS cc_start: 0.7552 (tttt) cc_final: 0.7296 (mttp) REVERT: D 146 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.6990 (mmp-170) REVERT: D 175 LYS cc_start: 0.7554 (tttt) cc_final: 0.7296 (mttp) outliers start: 24 outliers final: 12 residues processed: 176 average time/residue: 0.1785 time to fit residues: 42.3376 Evaluate side-chains 168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 303 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 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 = 0.3212 r_free = 0.3212 target = 0.122909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.105038 restraints weight = 8529.894| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.54 r_work: 0.2880 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7588 Z= 0.181 Angle : 0.638 7.365 10348 Z= 0.317 Chirality : 0.041 0.129 1156 Planarity : 0.005 0.045 1300 Dihedral : 6.066 49.643 1072 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.76 % Allowed : 14.92 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 968 helix: 1.58 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 289 HIS 0.001 0.000 HIS B 128 PHE 0.016 0.002 PHE D 140 TYR 0.021 0.002 TYR C 306 ARG 0.001 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 544) hydrogen bonds : angle 4.94326 ( 1632) covalent geometry : bond 0.00419 ( 7588) covalent geometry : angle 0.63790 (10348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7092 (mmp-170) REVERT: A 175 LYS cc_start: 0.7557 (tttt) cc_final: 0.7287 (mttp) REVERT: B 146 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7092 (mmp-170) REVERT: B 175 LYS cc_start: 0.7561 (tttt) cc_final: 0.7285 (mttp) REVERT: C 146 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7079 (mmp-170) REVERT: C 175 LYS cc_start: 0.7552 (tttt) cc_final: 0.7280 (mttp) REVERT: D 146 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7081 (mmp-170) REVERT: D 175 LYS cc_start: 0.7564 (tttt) cc_final: 0.7287 (mttp) outliers start: 20 outliers final: 12 residues processed: 172 average time/residue: 0.1912 time to fit residues: 44.3186 Evaluate side-chains 172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 303 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 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 = 0.3279 r_free = 0.3279 target = 0.128304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.110356 restraints weight = 8273.121| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.54 r_work: 0.2947 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7588 Z= 0.123 Angle : 0.603 7.600 10348 Z= 0.293 Chirality : 0.039 0.126 1156 Planarity : 0.005 0.044 1300 Dihedral : 5.712 47.031 1072 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.21 % Allowed : 16.02 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 968 helix: 1.78 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.79 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 289 HIS 0.001 0.000 HIS D 177 PHE 0.013 0.001 PHE A 140 TYR 0.019 0.001 TYR B 306 ARG 0.001 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 544) hydrogen bonds : angle 4.69126 ( 1632) covalent geometry : bond 0.00267 ( 7588) covalent geometry : angle 0.60308 (10348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.749 Fit side-chains REVERT: A 146 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7151 (mmp-170) REVERT: A 147 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7915 (tttp) REVERT: A 175 LYS cc_start: 0.7434 (tttt) cc_final: 0.7209 (mttp) REVERT: B 146 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7155 (mmp-170) REVERT: B 147 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7910 (tttp) REVERT: B 175 LYS cc_start: 0.7441 (tttt) cc_final: 0.7211 (mttp) REVERT: C 146 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7147 (mmp-170) REVERT: C 147 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7913 (tttp) REVERT: C 175 LYS cc_start: 0.7435 (tttt) cc_final: 0.7211 (mttp) REVERT: D 146 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7152 (mmp-170) REVERT: D 147 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7923 (tttp) REVERT: D 175 LYS cc_start: 0.7437 (tttt) cc_final: 0.7205 (mttp) outliers start: 16 outliers final: 12 residues processed: 180 average time/residue: 0.1881 time to fit residues: 46.0262 Evaluate side-chains 168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 229 ASN Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 303 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 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 = 0.3265 r_free = 0.3265 target = 0.127712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.109649 restraints weight = 8364.716| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.56 r_work: 0.2935 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7588 Z= 0.131 Angle : 0.624 8.425 10348 Z= 0.298 Chirality : 0.039 0.124 1156 Planarity : 0.005 0.044 1300 Dihedral : 5.684 46.671 1072 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.04 % Allowed : 15.75 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.27), residues: 968 helix: 1.81 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.79 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 289 HIS 0.001 0.000 HIS C 177 PHE 0.013 0.001 PHE D 140 TYR 0.021 0.002 TYR B 306 ARG 0.001 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 544) hydrogen bonds : angle 4.69253 ( 1632) covalent geometry : bond 0.00292 ( 7588) covalent geometry : angle 0.62449 (10348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.763 Fit side-chains REVERT: A 146 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7172 (mmp-170) REVERT: A 147 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7932 (tttp) REVERT: A 175 LYS cc_start: 0.7458 (tttt) cc_final: 0.7246 (mttp) REVERT: B 146 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7173 (mmp-170) REVERT: B 147 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7922 (tttp) REVERT: B 175 LYS cc_start: 0.7462 (tttt) cc_final: 0.7244 (mttp) REVERT: C 146 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7171 (mmp-170) REVERT: C 147 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7927 (tttp) REVERT: C 175 LYS cc_start: 0.7471 (tttt) cc_final: 0.7252 (mttp) REVERT: D 146 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7172 (mmp-170) REVERT: D 147 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7933 (tttp) REVERT: D 175 LYS cc_start: 0.7467 (tttt) cc_final: 0.7247 (mttp) outliers start: 22 outliers final: 18 residues processed: 176 average time/residue: 0.1881 time to fit residues: 44.7614 Evaluate side-chains 178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 229 ASN Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 303 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 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 = 0.3218 r_free = 0.3218 target = 0.123751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.105492 restraints weight = 8509.692| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.57 r_work: 0.2886 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7588 Z= 0.181 Angle : 0.677 9.909 10348 Z= 0.321 Chirality : 0.041 0.130 1156 Planarity : 0.005 0.045 1300 Dihedral : 5.941 49.165 1072 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.04 % Allowed : 16.30 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 968 helix: 1.66 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 192 HIS 0.001 0.001 HIS A 128 PHE 0.017 0.002 PHE C 246 TYR 0.025 0.002 TYR C 306 ARG 0.002 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 544) hydrogen bonds : angle 4.88627 ( 1632) covalent geometry : bond 0.00423 ( 7588) covalent geometry : angle 0.67675 (10348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.723 Fit side-chains REVERT: A 116 MET cc_start: 0.8827 (mmm) cc_final: 0.8535 (mmt) REVERT: A 146 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7186 (mmp-170) REVERT: A 147 LYS cc_start: 0.8373 (mtmm) cc_final: 0.8012 (tttp) REVERT: B 116 MET cc_start: 0.8826 (mmm) cc_final: 0.8530 (mmt) REVERT: B 146 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7189 (mmp-170) REVERT: B 147 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8003 (tttp) REVERT: C 116 MET cc_start: 0.8831 (mmm) cc_final: 0.8542 (mmt) REVERT: C 146 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7179 (mmp-170) REVERT: C 147 LYS cc_start: 0.8371 (mtmm) cc_final: 0.8004 (tttp) REVERT: D 116 MET cc_start: 0.8832 (mmm) cc_final: 0.8540 (mmt) REVERT: D 146 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7187 (mmp-170) REVERT: D 147 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8013 (tttp) outliers start: 22 outliers final: 14 residues processed: 172 average time/residue: 0.1883 time to fit residues: 43.6987 Evaluate side-chains 170 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 303 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 70 optimal weight: 0.0470 chunk 61 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 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 = 0.3270 r_free = 0.3270 target = 0.128145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.110215 restraints weight = 8375.389| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.55 r_work: 0.2951 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7588 Z= 0.127 Angle : 0.640 9.916 10348 Z= 0.301 Chirality : 0.039 0.123 1156 Planarity : 0.005 0.045 1300 Dihedral : 5.699 47.579 1072 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.49 % Allowed : 17.82 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 968 helix: 1.79 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.66 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 289 HIS 0.001 0.000 HIS B 177 PHE 0.013 0.001 PHE C 140 TYR 0.021 0.002 TYR B 306 ARG 0.001 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 544) hydrogen bonds : angle 4.71570 ( 1632) covalent geometry : bond 0.00282 ( 7588) covalent geometry : angle 0.63952 (10348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.710 Fit side-chains REVERT: A 116 MET cc_start: 0.8797 (mmm) cc_final: 0.8508 (mmt) REVERT: A 146 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7178 (mmp-170) REVERT: A 147 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7922 (tttp) REVERT: B 116 MET cc_start: 0.8801 (mmm) cc_final: 0.8512 (mmt) REVERT: B 146 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7180 (mmp-170) REVERT: B 147 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7911 (tttp) REVERT: C 116 MET cc_start: 0.8804 (mmm) cc_final: 0.8521 (mmt) REVERT: C 146 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7179 (mmp-170) REVERT: C 147 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7918 (tttp) REVERT: D 116 MET cc_start: 0.8808 (mmm) cc_final: 0.8523 (mmt) REVERT: D 146 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7175 (mmp-170) REVERT: D 147 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7925 (tttp) outliers start: 18 outliers final: 12 residues processed: 172 average time/residue: 0.1885 time to fit residues: 43.7087 Evaluate side-chains 168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 303 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 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 = 0.3216 r_free = 0.3216 target = 0.123642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.105657 restraints weight = 8437.318| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.54 r_work: 0.2883 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7588 Z= 0.185 Angle : 0.677 9.477 10348 Z= 0.322 Chirality : 0.041 0.129 1156 Planarity : 0.005 0.045 1300 Dihedral : 5.987 50.292 1072 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.49 % Allowed : 17.96 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 968 helix: 1.59 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 192 HIS 0.002 0.001 HIS A 128 PHE 0.017 0.002 PHE C 246 TYR 0.025 0.002 TYR B 306 ARG 0.002 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 544) hydrogen bonds : angle 4.91605 ( 1632) covalent geometry : bond 0.00434 ( 7588) covalent geometry : angle 0.67712 (10348) =============================================================================== Job complete usr+sys time: 3262.05 seconds wall clock time: 57 minutes 8.55 seconds (3428.55 seconds total)