Starting phenix.real_space_refine on Wed Feb 12 06:17:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ofz_16864/02_2025/8ofz_16864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ofz_16864/02_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_16864/02_2025/8ofz_16864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ofz_16864/02_2025/8ofz_16864.map" model { file = "/net/cci-nas-00/data/ceres_data/8ofz_16864/02_2025/8ofz_16864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ofz_16864/02_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-5592/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: 3.45, per 1000 atoms: 0.47 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: 1.72 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: 0.67 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: 2.25 Time building geometry restraints manager: 1.92 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: 0.080 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 18.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- 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= 0.633 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 *********************** 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 : 0.727 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: 0.1888 time to fit residues: 46.6926 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 : 0.703 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.111983 restraints weight = 8152.876| |-----------------------------------------------------------------------------| 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: 0.2847 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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= 0.207 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 *********************** 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 : 0.893 Fit side-chains REVERT: A 146 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6970 (mmp-170) REVERT: A 175 LYS cc_start: 0.7686 (tttt) cc_final: 0.7087 (mttp) REVERT: A 177 HIS cc_start: 0.8015 (t70) cc_final: 0.7760 (t-90) REVERT: B 146 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6973 (mmp-170) REVERT: B 175 LYS cc_start: 0.7689 (tttt) cc_final: 0.7093 (mttp) REVERT: B 177 HIS cc_start: 0.8022 (t70) cc_final: 0.7763 (t-90) REVERT: C 146 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6972 (mmp-170) REVERT: C 175 LYS cc_start: 0.7682 (tttt) cc_final: 0.7093 (mttp) REVERT: C 177 HIS cc_start: 0.8018 (t70) cc_final: 0.7757 (t-90) REVERT: D 146 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6967 (mmp-170) REVERT: D 175 LYS cc_start: 0.7700 (tttt) cc_final: 0.7101 (mttp) REVERT: D 177 HIS cc_start: 0.8025 (t70) cc_final: 0.7771 (t-90) outliers start: 8 outliers final: 4 residues processed: 180 average time/residue: 0.1733 time to fit residues: 42.9264 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 : 0.702 ------------------------------------------------------------------------------- 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: 0.5980 chunk 79 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 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 = 0.3299 r_free = 0.3299 target = 0.129564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.112746 restraints weight = 8321.096| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.49 r_work: 0.2984 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7588 Z= 0.191 Angle : 0.580 5.815 10348 Z= 0.304 Chirality : 0.039 0.121 1156 Planarity : 0.005 0.039 1300 Dihedral : 6.999 51.216 1080 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.74 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: 1.13 (0.26), residues: 968 helix: 1.89 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.91 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 289 HIS 0.001 0.001 HIS B 177 PHE 0.016 0.002 PHE D 140 TYR 0.012 0.001 TYR C 206 ARG 0.002 0.001 ARG D 72 *********************** 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 : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6890 (mmp-170) REVERT: A 175 LYS cc_start: 0.7625 (tttt) cc_final: 0.7253 (mttp) REVERT: B 146 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6889 (mmp-170) REVERT: B 175 LYS cc_start: 0.7607 (tttt) cc_final: 0.7227 (mttp) REVERT: C 146 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6889 (mmp-170) REVERT: C 175 LYS cc_start: 0.7609 (tttt) cc_final: 0.7239 (mttp) REVERT: D 146 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6891 (mmp-170) REVERT: D 175 LYS cc_start: 0.7615 (tttt) cc_final: 0.7242 (mttp) outliers start: 8 outliers final: 4 residues processed: 176 average time/residue: 0.1941 time to fit residues: 45.7160 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 : 0.783 ------------------------------------------------------------------------------- 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: 0.0570 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7302 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.131232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.114629 restraints weight = 8234.063| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.51 r_work: 0.3016 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2886 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= 0.166 Angle : 0.570 6.421 10348 Z= 0.288 Chirality : 0.038 0.117 1156 Planarity : 0.005 0.040 1300 Dihedral : 6.511 45.872 1080 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.66 % Allowed : 11.60 % Favored : 86.74 % 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: 1.99 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.93 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 289 HIS 0.004 0.001 HIS B 177 PHE 0.013 0.001 PHE A 140 TYR 0.009 0.001 TYR D 206 ARG 0.001 0.000 ARG A 72 *********************** 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 192 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.677 Fit side-chains REVERT: A 146 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7031 (mmp-170) REVERT: A 147 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7745 (mttt) REVERT: A 175 LYS cc_start: 0.7491 (tttt) cc_final: 0.7225 (mttp) REVERT: B 146 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7036 (mmp-170) REVERT: B 147 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7746 (mttt) REVERT: B 175 LYS cc_start: 0.7492 (tttt) cc_final: 0.7229 (mttp) REVERT: C 146 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7029 (mmp-170) REVERT: C 147 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7740 (mttt) REVERT: C 175 LYS cc_start: 0.7503 (tttt) cc_final: 0.7247 (mttp) REVERT: D 146 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7031 (mmp-170) REVERT: D 147 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7744 (mttt) REVERT: D 175 LYS cc_start: 0.7500 (tttt) cc_final: 0.7236 (mttp) outliers start: 12 outliers final: 0 residues processed: 188 average time/residue: 0.1935 time to fit residues: 49.3223 Evaluate side-chains 152 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain D residue 146 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 79 optimal weight: 0.0770 chunk 59 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.130337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.113361 restraints weight = 8165.849| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.50 r_work: 0.2992 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3018 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= 0.174 Angle : 0.574 6.425 10348 Z= 0.288 Chirality : 0.039 0.122 1156 Planarity : 0.005 0.042 1300 Dihedral : 5.630 44.411 1072 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.21 % Allowed : 14.36 % Favored : 83.43 % 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: 1.37 (0.27), residues: 968 helix: 2.05 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 289 HIS 0.000 0.000 HIS B 283 PHE 0.014 0.001 PHE A 140 TYR 0.012 0.001 TYR A 306 ARG 0.001 0.000 ARG A 72 *********************** 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 180 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.794 Fit side-chains REVERT: A 146 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7119 (mmp-170) REVERT: A 147 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7875 (tttp) REVERT: B 146 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7115 (mmp-170) REVERT: B 147 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7876 (tttp) REVERT: C 146 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7109 (mmp-170) REVERT: C 147 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7872 (tttp) REVERT: D 146 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7113 (mmp-170) REVERT: D 147 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7886 (tttp) outliers start: 16 outliers final: 4 residues processed: 180 average time/residue: 0.2030 time to fit residues: 48.5474 Evaluate side-chains 164 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 146 ARG 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: 0.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 13 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3324 r_free = 0.3324 target = 0.132462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.115504 restraints weight = 8265.523| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.50 r_work: 0.3020 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7588 Z= 0.162 Angle : 0.559 6.215 10348 Z= 0.281 Chirality : 0.038 0.121 1156 Planarity : 0.005 0.041 1300 Dihedral : 5.543 43.205 1072 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.21 % Allowed : 14.92 % 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: 1.54 (0.27), residues: 968 helix: 2.16 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.62 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 289 HIS 0.001 0.000 HIS D 177 PHE 0.012 0.001 PHE A 140 TYR 0.018 0.002 TYR D 306 ARG 0.001 0.000 ARG B 72 *********************** 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 184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.720 Fit side-chains REVERT: A 116 MET cc_start: 0.8767 (mmm) cc_final: 0.8495 (mmt) REVERT: A 146 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7119 (mmp-170) REVERT: A 147 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7955 (tttp) REVERT: B 116 MET cc_start: 0.8762 (mmm) cc_final: 0.8493 (mmt) REVERT: B 146 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7115 (mmp-170) REVERT: B 147 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7951 (tttp) REVERT: C 116 MET cc_start: 0.8766 (mmm) cc_final: 0.8495 (mmt) REVERT: C 146 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7105 (mmp-170) REVERT: C 147 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7948 (tttp) REVERT: D 116 MET cc_start: 0.8768 (mmm) cc_final: 0.8495 (mmt) REVERT: D 146 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7111 (mmp-170) REVERT: D 147 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7952 (tttp) outliers start: 16 outliers final: 8 residues processed: 180 average time/residue: 0.1917 time to fit residues: 46.4841 Evaluate side-chains 168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 229 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 303 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 229 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: 0.9980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.128948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.112009 restraints weight = 8353.459| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.50 r_work: 0.2984 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3337 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= 0.193 Angle : 0.589 7.567 10348 Z= 0.292 Chirality : 0.039 0.121 1156 Planarity : 0.005 0.043 1300 Dihedral : 5.640 43.966 1072 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.21 % Allowed : 14.92 % 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: 1.47 (0.27), residues: 968 helix: 2.06 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.53 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 289 HIS 0.001 0.000 HIS B 283 PHE 0.014 0.002 PHE C 246 TYR 0.020 0.002 TYR C 306 ARG 0.001 0.000 ARG B 72 *********************** 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 172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.833 Fit side-chains REVERT: A 146 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7149 (mmp-170) REVERT: A 147 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7982 (tttp) REVERT: B 146 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7142 (mmp-170) REVERT: B 147 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7975 (tttp) REVERT: C 146 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7136 (mmp-170) REVERT: C 147 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7972 (tttp) REVERT: D 146 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7140 (mmp-170) REVERT: D 147 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7976 (tttp) outliers start: 16 outliers final: 4 residues processed: 172 average time/residue: 0.1945 time to fit residues: 44.9387 Evaluate side-chains 164 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 146 ARG 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: 2.9990 chunk 78 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.125064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.108153 restraints weight = 8514.294| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.46 r_work: 0.2921 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3270 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= 0.260 Angle : 0.623 7.900 10348 Z= 0.310 Chirality : 0.040 0.130 1156 Planarity : 0.005 0.044 1300 Dihedral : 5.842 45.676 1072 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.21 % Allowed : 16.57 % 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: 1.10 (0.26), residues: 968 helix: 1.71 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.77 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 192 HIS 0.001 0.000 HIS C 128 PHE 0.018 0.002 PHE A 246 TYR 0.023 0.002 TYR B 306 ARG 0.001 0.000 ARG D 72 *********************** 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 172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.820 Fit side-chains REVERT: A 146 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7186 (mmp-170) REVERT: A 147 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8039 (tttp) REVERT: B 146 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7189 (mmp-170) REVERT: B 147 LYS cc_start: 0.8376 (mtmm) cc_final: 0.8039 (tttp) REVERT: C 146 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7181 (mmp-170) REVERT: C 147 LYS cc_start: 0.8376 (mtmm) cc_final: 0.8034 (tttp) REVERT: D 146 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7181 (mmp-170) REVERT: D 147 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8033 (tttp) outliers start: 16 outliers final: 8 residues processed: 168 average time/residue: 0.1937 time to fit residues: 44.0189 Evaluate side-chains 168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 229 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 303 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 229 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: 6.9990 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.125252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.107960 restraints weight = 8557.882| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.52 r_work: 0.2927 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3352 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= 0.222 Angle : 0.611 8.249 10348 Z= 0.302 Chirality : 0.040 0.126 1156 Planarity : 0.005 0.044 1300 Dihedral : 5.771 45.614 1072 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.66 % Allowed : 17.13 % 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: 1.15 (0.26), residues: 968 helix: 1.73 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.72 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 289 HIS 0.001 0.000 HIS D 128 PHE 0.014 0.002 PHE D 140 TYR 0.022 0.002 TYR B 306 ARG 0.001 0.000 ARG B 72 *********************** 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 176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.826 Fit side-chains REVERT: A 146 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7186 (mmp-170) REVERT: A 147 LYS cc_start: 0.8326 (mtmm) cc_final: 0.7993 (tttp) REVERT: B 146 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7184 (mmp-170) REVERT: B 147 LYS cc_start: 0.8316 (mtmm) cc_final: 0.7979 (tttp) REVERT: C 146 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7173 (mmp-170) REVERT: C 147 LYS cc_start: 0.8317 (mtmm) cc_final: 0.7977 (tttp) REVERT: D 146 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7179 (mmp-170) REVERT: D 147 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7986 (tttp) outliers start: 12 outliers final: 8 residues processed: 176 average time/residue: 0.1937 time to fit residues: 45.8673 Evaluate side-chains 172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 229 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 303 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 229 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 20 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 70 optimal weight: 0.0070 chunk 61 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.123334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.105683 restraints weight = 8549.048| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.50 r_work: 0.2889 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7588 Z= 0.269 Angle : 0.631 8.421 10348 Z= 0.314 Chirality : 0.040 0.131 1156 Planarity : 0.005 0.047 1300 Dihedral : 5.960 47.421 1072 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.21 % Allowed : 17.68 % Favored : 80.11 % 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: 1.15 (0.26), residues: 968 helix: 1.71 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 192 HIS 0.002 0.001 HIS D 128 PHE 0.018 0.002 PHE B 246 TYR 0.026 0.002 TYR A 306 ARG 0.002 0.000 ARG A 72 ********************** 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 180 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.720 Fit side-chains REVERT: A 103 LEU cc_start: 0.8592 (mt) cc_final: 0.8375 (mt) REVERT: A 146 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7209 (mmp-170) REVERT: A 147 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8020 (tttp) REVERT: B 103 LEU cc_start: 0.8594 (mt) cc_final: 0.8377 (mt) REVERT: B 146 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7216 (mmp-170) REVERT: B 147 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8024 (tttp) REVERT: C 103 LEU cc_start: 0.8591 (mt) cc_final: 0.8375 (mt) REVERT: C 146 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7211 (mmp-170) REVERT: C 147 LYS cc_start: 0.8378 (mtmm) cc_final: 0.8018 (tttp) REVERT: D 103 LEU cc_start: 0.8601 (mt) cc_final: 0.8379 (mt) REVERT: D 146 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7212 (mmp-170) REVERT: D 147 LYS cc_start: 0.8378 (mtmm) cc_final: 0.8020 (tttp) outliers start: 16 outliers final: 8 residues processed: 176 average time/residue: 0.1927 time to fit residues: 45.7348 Evaluate side-chains 172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 229 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 303 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 229 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: 5.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 64 optimal weight: 0.0020 overall best weight: 1.9994 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.124840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.107178 restraints weight = 8416.755| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.49 r_work: 0.2914 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7588 Z= 0.242 Angle : 0.646 8.294 10348 Z= 0.313 Chirality : 0.040 0.130 1156 Planarity : 0.006 0.054 1300 Dihedral : 5.877 47.315 1072 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.66 % Allowed : 18.78 % 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: 1.23 (0.27), residues: 968 helix: 1.76 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 192 HIS 0.001 0.000 HIS C 128 PHE 0.015 0.002 PHE D 140 TYR 0.024 0.002 TYR B 306 ARG 0.002 0.000 ARG A 72 =============================================================================== Job complete usr+sys time: 3112.94 seconds wall clock time: 56 minutes 22.55 seconds (3382.55 seconds total)