Starting phenix.real_space_refine on Thu Nov 14 21:06:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofz_16864/11_2024/8ofz_16864.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofz_16864/11_2024/8ofz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofz_16864/11_2024/8ofz_16864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofz_16864/11_2024/8ofz_16864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofz_16864/11_2024/8ofz_16864.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ofz_16864/11_2024/8ofz_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-5513/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: 3.59, per 1000 atoms: 0.49 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: 1.92 Conformation dependent library (CDL) restraints added in 1.2 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: 0.66 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: 2.13 Time building geometry restraints manager: 2.16 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 19.460 Find NCS groups from input model: 0.270 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- 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 : 0.804 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: 0.1934 time to fit residues: 47.8414 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 : 0.825 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5712 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 : 1.381 Fit side-chains REVERT: A 146 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.5793 (mmp-170) REVERT: A 175 LYS cc_start: 0.5545 (tttt) cc_final: 0.5339 (mttp) REVERT: B 146 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.5792 (mmp-170) REVERT: B 175 LYS cc_start: 0.5545 (tttt) cc_final: 0.5339 (mttp) REVERT: C 146 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.5793 (mmp-170) REVERT: C 175 LYS cc_start: 0.5547 (tttt) cc_final: 0.5340 (mttp) REVERT: D 146 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.5794 (mmp-170) REVERT: D 175 LYS cc_start: 0.5545 (tttt) cc_final: 0.5339 (mttp) outliers start: 8 outliers final: 4 residues processed: 180 average time/residue: 0.1893 time to fit residues: 46.5055 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 : 0.814 ------------------------------------------------------------------------------- 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 48 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 0.0010 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 0.0060 chunk 70 optimal weight: 0.1980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.2681 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= 0.164 Angle : 0.566 5.800 10348 Z= 0.296 Chirality : 0.039 0.115 1156 Planarity : 0.005 0.038 1300 Dihedral : 6.792 48.327 1080 Min Nonbonded Distance : 2.526 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: 1.24 (0.26), residues: 968 helix: 1.99 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.90 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 289 HIS 0.002 0.000 HIS C 283 PHE 0.013 0.001 PHE A 140 TYR 0.010 0.001 TYR D 206 ARG 0.001 0.001 ARG A 269 *********************** 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 184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.912 Fit side-chains REVERT: A 146 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.5723 (mmp-170) REVERT: A 260 MET cc_start: 0.8003 (mtm) cc_final: 0.7612 (mtm) REVERT: B 146 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.5723 (mmp-170) REVERT: B 260 MET cc_start: 0.8002 (mtm) cc_final: 0.7612 (mtm) REVERT: C 146 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.5723 (mmp-170) REVERT: C 260 MET cc_start: 0.8003 (mtm) cc_final: 0.7612 (mtm) REVERT: D 146 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.5722 (mmp-170) REVERT: D 260 MET cc_start: 0.8002 (mtm) cc_final: 0.7611 (mtm) outliers start: 8 outliers final: 4 residues processed: 180 average time/residue: 0.1913 time to fit residues: 46.4436 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 : 0.842 ------------------------------------------------------------------------------- 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 86 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 0.2941 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= 0.229 Angle : 0.617 8.372 10348 Z= 0.306 Chirality : 0.040 0.126 1156 Planarity : 0.005 0.042 1300 Dihedral : 6.727 46.614 1080 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.66 % Allowed : 13.26 % Favored : 85.08 % 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: 1.12 (0.26), residues: 968 helix: 1.87 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.88 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 289 HIS 0.001 0.000 HIS A 128 PHE 0.017 0.002 PHE D 246 TYR 0.013 0.002 TYR A 306 ARG 0.001 0.000 ARG A 146 *********************** 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 176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.806 Fit side-chains REVERT: A 146 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6168 (mmp-170) REVERT: A 312 HIS cc_start: 0.3846 (OUTLIER) cc_final: 0.3584 (m-70) REVERT: B 146 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6168 (mmp-170) REVERT: B 312 HIS cc_start: 0.3847 (OUTLIER) cc_final: 0.3582 (m-70) REVERT: C 146 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6168 (mmp-170) REVERT: C 312 HIS cc_start: 0.3846 (OUTLIER) cc_final: 0.3583 (m-70) REVERT: D 146 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6168 (mmp-170) REVERT: D 312 HIS cc_start: 0.3847 (OUTLIER) cc_final: 0.3583 (m-70) outliers start: 12 outliers final: 0 residues processed: 176 average time/residue: 0.1905 time to fit residues: 45.2110 Evaluate side-chains 166 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 0.0020 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5717 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7588 Z= 0.160 Angle : 0.603 7.516 10348 Z= 0.296 Chirality : 0.038 0.120 1156 Planarity : 0.005 0.042 1300 Dihedral : 6.501 45.685 1080 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.66 % Allowed : 13.81 % Favored : 84.53 % 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: 1.33 (0.27), residues: 968 helix: 1.98 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -1.72 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 289 HIS 0.001 0.000 HIS A 312 PHE 0.013 0.001 PHE D 140 TYR 0.015 0.001 TYR A 306 ARG 0.001 0.001 ARG C 146 *********************** 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: 12 poor density : 168 time to evaluate : 0.724 Fit side-chains REVERT: A 146 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6126 (mmp-170) REVERT: B 146 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6126 (mmp-170) REVERT: C 146 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6126 (mmp-170) REVERT: D 146 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6127 (mmp-170) outliers start: 12 outliers final: 4 residues processed: 180 average time/residue: 0.1921 time to fit residues: 46.7254 Evaluate side-chains 160 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 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 : 0.003 0.022 7588 Z= 0.206 Angle : 0.610 7.247 10348 Z= 0.301 Chirality : 0.039 0.122 1156 Planarity : 0.005 0.043 1300 Dihedral : 5.842 44.758 1072 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.21 % Allowed : 15.47 % 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: 1.27 (0.27), residues: 968 helix: 1.97 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.76 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 289 HIS 0.000 0.000 HIS C 312 PHE 0.015 0.002 PHE B 246 TYR 0.020 0.002 TYR B 306 ARG 0.001 0.000 ARG C 146 *********************** 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 174 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.826 Fit side-chains REVERT: A 146 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6080 (mmp-170) REVERT: B 146 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6079 (mmp-170) REVERT: C 146 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6080 (mmp-170) REVERT: D 146 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6080 (mmp-170) outliers start: 16 outliers final: 8 residues processed: 170 average time/residue: 0.1963 time to fit residues: 44.7588 Evaluate side-chains 166 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG 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 261 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 146 ARG 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 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 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.3534 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= 0.164 Angle : 0.594 7.694 10348 Z= 0.291 Chirality : 0.038 0.121 1156 Planarity : 0.005 0.042 1300 Dihedral : 5.661 43.427 1072 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.21 % Allowed : 17.13 % 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: 1.45 (0.27), residues: 968 helix: 2.11 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 289 HIS 0.000 0.000 HIS D 283 PHE 0.013 0.001 PHE D 140 TYR 0.019 0.001 TYR B 306 ARG 0.001 0.001 ARG D 146 *********************** 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 : 1.024 Fit side-chains REVERT: A 146 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.5935 (mmp-170) REVERT: B 146 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.5934 (mmp-170) REVERT: C 146 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.5935 (mmp-170) REVERT: D 146 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.5934 (mmp-170) outliers start: 16 outliers final: 8 residues processed: 168 average time/residue: 0.2107 time to fit residues: 47.8874 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 : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG 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 261 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 146 ARG 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 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 27 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7588 Z= 0.226 Angle : 0.621 8.404 10348 Z= 0.305 Chirality : 0.039 0.124 1156 Planarity : 0.005 0.044 1300 Dihedral : 5.781 44.110 1072 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.21 % Allowed : 17.13 % 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: 1.32 (0.27), residues: 968 helix: 2.00 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.71 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 192 HIS 0.001 0.000 HIS A 128 PHE 0.017 0.002 PHE A 246 TYR 0.023 0.002 TYR B 306 ARG 0.001 0.000 ARG D 146 *********************** 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 184 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.806 Fit side-chains REVERT: A 77 GLU cc_start: 0.6795 (tp30) cc_final: 0.6201 (tp30) REVERT: A 146 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.5988 (mmp-170) REVERT: B 77 GLU cc_start: 0.6795 (tp30) cc_final: 0.6200 (tp30) REVERT: B 146 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.5987 (mmp-170) REVERT: C 77 GLU cc_start: 0.6794 (tp30) cc_final: 0.6200 (tp30) REVERT: C 146 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.5986 (mmp-170) REVERT: D 77 GLU cc_start: 0.6794 (tp30) cc_final: 0.6200 (tp30) REVERT: D 146 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.5987 (mmp-170) outliers start: 16 outliers final: 12 residues processed: 180 average time/residue: 0.2064 time to fit residues: 49.2669 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 : 0.749 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 0.3693 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= 0.158 Angle : 0.606 7.716 10348 Z= 0.291 Chirality : 0.038 0.119 1156 Planarity : 0.005 0.043 1300 Dihedral : 5.543 42.404 1072 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.21 % Allowed : 16.85 % Favored : 80.94 % 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: 1.51 (0.27), residues: 968 helix: 2.18 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.75 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 289 HIS 0.001 0.000 HIS C 177 PHE 0.013 0.001 PHE A 140 TYR 0.019 0.001 TYR B 306 ARG 0.001 0.000 ARG D 146 *********************** 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 180 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.865 Fit side-chains REVERT: A 77 GLU cc_start: 0.6787 (tp30) cc_final: 0.6260 (tp30) REVERT: A 146 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.5871 (tpp-160) REVERT: B 77 GLU cc_start: 0.6786 (tp30) cc_final: 0.6259 (tp30) REVERT: B 146 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.5871 (tpp-160) REVERT: C 77 GLU cc_start: 0.6789 (tp30) cc_final: 0.6260 (tp30) REVERT: C 146 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.5870 (tpp-160) REVERT: D 77 GLU cc_start: 0.6791 (tp30) cc_final: 0.6261 (tp30) REVERT: D 146 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.5871 (tpp-160) outliers start: 16 outliers final: 12 residues processed: 176 average time/residue: 0.1981 time to fit residues: 46.8459 Evaluate side-chains 176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.3761 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= 0.165 Angle : 0.600 7.766 10348 Z= 0.287 Chirality : 0.038 0.117 1156 Planarity : 0.005 0.043 1300 Dihedral : 5.495 42.534 1072 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.21 % Allowed : 17.13 % 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: 1.63 (0.27), residues: 968 helix: 2.27 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -1.71 (0.35), 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 0.012 0.001 PHE B 140 TYR 0.020 0.001 TYR C 306 ARG 0.001 0.000 ARG D 146 ********************** 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 176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.796 Fit side-chains REVERT: A 71 TYR cc_start: 0.6865 (m-10) cc_final: 0.6630 (m-80) REVERT: A 77 GLU cc_start: 0.6798 (tp30) cc_final: 0.6299 (tp30) REVERT: A 146 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.5730 (tpp-160) REVERT: B 71 TYR cc_start: 0.6866 (m-10) cc_final: 0.6632 (m-80) REVERT: B 77 GLU cc_start: 0.6798 (tp30) cc_final: 0.6298 (tp30) REVERT: B 146 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.5730 (tpp-160) REVERT: C 71 TYR cc_start: 0.6866 (m-10) cc_final: 0.6632 (m-80) REVERT: C 77 GLU cc_start: 0.6801 (tp30) cc_final: 0.6297 (tp30) REVERT: C 146 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.5730 (tpp-160) REVERT: D 71 TYR cc_start: 0.6865 (m-10) cc_final: 0.6629 (m-80) REVERT: D 77 GLU cc_start: 0.6801 (tp30) cc_final: 0.6297 (tp30) REVERT: D 146 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.5732 (tpp-160) outliers start: 16 outliers final: 10 residues processed: 172 average time/residue: 0.2027 time to fit residues: 47.0173 Evaluate side-chains 170 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 78 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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** ** D 250 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 = 0.3317 r_free = 0.3317 target = 0.132569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.115200 restraints weight = 8183.275| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.53 r_work: 0.3009 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7588 Z= 0.159 Angle : 0.599 7.825 10348 Z= 0.289 Chirality : 0.038 0.115 1156 Planarity : 0.005 0.043 1300 Dihedral : 5.422 42.529 1072 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.93 % Allowed : 17.13 % Favored : 80.94 % 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: 1.71 (0.27), residues: 968 helix: 2.29 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -1.63 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 289 HIS 0.000 0.000 HIS C 283 PHE 0.012 0.001 PHE C 140 TYR 0.019 0.001 TYR B 306 ARG 0.001 0.000 ARG B 72 =============================================================================== Job complete usr+sys time: 1763.48 seconds wall clock time: 32 minutes 57.65 seconds (1977.65 seconds total)