Starting phenix.real_space_refine on Wed Mar 5 18:37:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x84_33055/03_2025/7x84_33055.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x84_33055/03_2025/7x84_33055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x84_33055/03_2025/7x84_33055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x84_33055/03_2025/7x84_33055.map" model { file = "/net/cci-nas-00/data/ceres_data/7x84_33055/03_2025/7x84_33055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x84_33055/03_2025/7x84_33055.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 21 5.16 5 C 2082 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Restraints were copied for chains: C, B Time building chain proxies: 3.32, per 1000 atoms: 1.02 Number of scatterers: 3258 At special positions: 0 Unit cell: (99.6, 107.07, 33.2, 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 21 16.00 O 636 8.00 N 519 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.02 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: 0.79 Conformation dependent library (CDL) restraints added in 415.1 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 134 removed outlier: 6.992A pdb=" N VAL B 133 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 139 removed outlier: 6.438A pdb=" N GLN B 138 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN A 138 " --> pdb=" O LYS C 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 162 through 168 removed outlier: 6.865A pdb=" N ALA B 167 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN A 168 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA A 167 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN C 168 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.377A pdb=" N ILE B 176 " --> pdb=" O GLY A 177 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 176 " --> pdb=" O GLY C 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 180 through 186 removed outlier: 6.429A pdb=" N LEU B 181 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASN B 183 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ILE A 186 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N THR B 185 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU A 181 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN A 183 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N ILE C 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N THR A 185 " --> pdb=" O ILE C 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 197 through 198 removed outlier: 6.664A pdb=" N TYR B 197 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR A 197 " --> pdb=" O THR C 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB2, first strand: chain 'B' and resid 215 through 221 removed outlier: 6.645A pdb=" N THR B 215 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N SER A 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 217 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LYS A 220 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ILE B 219 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR A 215 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N SER C 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 217 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LYS C 220 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ILE A 219 " --> pdb=" O LYS C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 226 through 228 Processing sheet with id=AB4, first strand: chain 'B' and resid 235 through 238 removed outlier: 6.452A pdb=" N THR B 235 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLY A 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE B 237 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLY C 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AB6, first strand: chain 'B' and resid 251 through 252 32 hydrogen bonds defined for protein. 96 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: 0.76 Time building geometry restraints manager: 0.95 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: 1026 1.34 - 1.45: 518 1.45 - 1.57: 1732 1.57 - 1.69: 0 1.69 - 1.80: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CA THR C 234 " pdb=" CB THR C 234 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.35e-02 5.49e+03 3.76e+00 bond pdb=" CA THR B 234 " pdb=" CB THR B 234 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.35e-02 5.49e+03 3.40e+00 bond pdb=" CA THR A 234 " pdb=" CB THR A 234 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.35e-02 5.49e+03 3.21e+00 bond pdb=" CG1 ILE B 146 " pdb=" CD1 ILE B 146 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.32e+00 bond pdb=" CG1 ILE A 146 " pdb=" CD1 ILE A 146 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.30e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 4370 2.08 - 4.16: 121 4.16 - 6.24: 9 6.24 - 8.32: 0 8.32 - 10.40: 3 Bond angle restraints: 4503 Sorted by residual: angle pdb=" N THR C 234 " pdb=" CA THR C 234 " pdb=" C THR C 234 " ideal model delta sigma weight residual 107.23 117.63 -10.40 1.67e+00 3.59e-01 3.87e+01 angle pdb=" N THR A 234 " pdb=" CA THR A 234 " pdb=" C THR A 234 " ideal model delta sigma weight residual 107.23 117.58 -10.35 1.67e+00 3.59e-01 3.84e+01 angle pdb=" N THR B 234 " pdb=" CA THR B 234 " pdb=" C THR B 234 " ideal model delta sigma weight residual 107.23 117.57 -10.34 1.67e+00 3.59e-01 3.83e+01 angle pdb=" C THR A 234 " pdb=" CA THR A 234 " pdb=" CB THR A 234 " ideal model delta sigma weight residual 111.42 106.84 4.58 1.31e+00 5.83e-01 1.22e+01 angle pdb=" C THR C 234 " pdb=" CA THR C 234 " pdb=" CB THR C 234 " ideal model delta sigma weight residual 111.42 106.84 4.58 1.31e+00 5.83e-01 1.22e+01 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 1763 15.39 - 30.77: 157 30.77 - 46.16: 63 46.16 - 61.54: 3 61.54 - 76.93: 3 Dihedral angle restraints: 1989 sinusoidal: 771 harmonic: 1218 Sorted by residual: dihedral pdb=" CA TYR C 135 " pdb=" C TYR C 135 " pdb=" N ASP C 136 " pdb=" CA ASP C 136 " ideal model delta harmonic sigma weight residual -180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA TYR B 135 " pdb=" C TYR B 135 " pdb=" N ASP B 136 " pdb=" CA ASP B 136 " ideal model delta harmonic sigma weight residual -180.00 -162.03 -17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA TYR A 135 " pdb=" C TYR A 135 " pdb=" N ASP A 136 " pdb=" CA ASP A 136 " ideal model delta harmonic sigma weight residual 180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 259 0.031 - 0.063: 146 0.063 - 0.094: 61 0.094 - 0.125: 62 0.125 - 0.156: 15 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB THR C 153 " pdb=" CA THR C 153 " pdb=" OG1 THR C 153 " pdb=" CG2 THR C 153 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB THR A 153 " pdb=" CA THR A 153 " pdb=" OG1 THR A 153 " pdb=" CG2 THR A 153 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CB THR B 153 " pdb=" CA THR B 153 " pdb=" OG1 THR B 153 " pdb=" CG2 THR B 153 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.022 2.00e-02 2.50e+03 1.93e-02 7.43e+00 pdb=" CG TYR C 143 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR C 143 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR C 143 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 143 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 143 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 143 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.022 2.00e-02 2.50e+03 1.92e-02 7.34e+00 pdb=" CG TYR A 143 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 143 " 0.021 2.00e-02 2.50e+03 1.91e-02 7.33e+00 pdb=" CG TYR B 143 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 143 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 143 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 143 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 143 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 143 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 143 " 0.002 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 34 2.60 - 3.17: 2806 3.17 - 3.75: 4494 3.75 - 4.32: 6645 4.32 - 4.90: 12475 Nonbonded interactions: 26454 Sorted by model distance: nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " model vdw 2.024 3.760 nonbonded pdb=" O ASN A 148 " pdb=" OG1 THR A 149 " model vdw 2.259 3.040 nonbonded pdb=" O ASN C 148 " pdb=" OG1 THR C 149 " model vdw 2.259 3.040 nonbonded pdb=" O ASN B 148 " pdb=" OG1 THR B 149 " model vdw 2.259 3.040 ... (remaining 26449 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.720 Find NCS groups from input model: 0.070 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:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.008 0.045 3312 Z= 0.528 Angle : 0.832 10.395 4503 Z= 0.490 Chirality : 0.056 0.156 543 Planarity : 0.003 0.020 558 Dihedral : 13.867 76.927 1206 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % 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: -5.69 (0.26), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.33 (0.20), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 239 PHE 0.005 0.002 PHE B 213 TYR 0.047 0.004 TYR C 143 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.379 Fit side-chains REVERT: B 124 LYS cc_start: 0.8599 (mtmt) cc_final: 0.7079 (mmpt) REVERT: B 140 ARG cc_start: 0.5415 (mtt180) cc_final: 0.4621 (ptm-80) REVERT: B 178 LYS cc_start: 0.7132 (mttm) cc_final: 0.5927 (pptt) REVERT: B 180 ARG cc_start: 0.7566 (mtt180) cc_final: 0.6598 (pmt170) REVERT: B 249 GLN cc_start: 0.7763 (tt0) cc_final: 0.7515 (tm-30) REVERT: B 252 ASP cc_start: 0.7812 (t0) cc_final: 0.7387 (t0) REVERT: A 178 LYS cc_start: 0.6965 (mttm) cc_final: 0.6550 (mtpt) REVERT: A 180 ARG cc_start: 0.7487 (mtt180) cc_final: 0.6897 (ttt180) REVERT: A 249 GLN cc_start: 0.7660 (tt0) cc_final: 0.7428 (tp40) REVERT: C 165 ILE cc_start: 0.8882 (mt) cc_final: 0.8649 (mt) REVERT: C 178 LYS cc_start: 0.7352 (mttm) cc_final: 0.6292 (mmpt) REVERT: C 180 ARG cc_start: 0.7374 (mtt180) cc_final: 0.6563 (tpm170) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 1.3971 time to fit residues: 135.7627 Evaluate side-chains 75 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 245 GLN A 148 ASN ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN C 148 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 245 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.142587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.127245 restraints weight = 4835.219| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.10 r_work: 0.3979 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3312 Z= 0.221 Angle : 0.635 5.986 4503 Z= 0.359 Chirality : 0.052 0.148 543 Planarity : 0.002 0.021 558 Dihedral : 6.057 19.752 447 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.65 % Allowed : 19.58 % Favored : 77.78 % 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: -4.75 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.005 0.001 PHE A 213 TYR 0.020 0.002 TYR A 143 ARG 0.001 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.358 Fit side-chains REVERT: B 124 LYS cc_start: 0.8677 (mtmt) cc_final: 0.7021 (mmpt) REVERT: B 140 ARG cc_start: 0.5294 (mtt180) cc_final: 0.4376 (ptm-80) REVERT: B 148 ASN cc_start: 0.7408 (m-40) cc_final: 0.6944 (t0) REVERT: B 178 LYS cc_start: 0.7043 (mttm) cc_final: 0.5660 (pptt) REVERT: B 180 ARG cc_start: 0.7831 (mtt180) cc_final: 0.6427 (pmt170) REVERT: B 190 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7870 (tt) REVERT: B 206 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 249 GLN cc_start: 0.8323 (tt0) cc_final: 0.7889 (tm-30) REVERT: B 252 ASP cc_start: 0.7956 (t0) cc_final: 0.7412 (t0) REVERT: A 148 ASN cc_start: 0.7316 (m-40) cc_final: 0.7090 (t0) REVERT: A 178 LYS cc_start: 0.6805 (mttm) cc_final: 0.6400 (mtpt) REVERT: A 180 ARG cc_start: 0.7788 (mtt180) cc_final: 0.6821 (ttt90) REVERT: A 205 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: A 249 GLN cc_start: 0.8171 (tt0) cc_final: 0.7897 (tm-30) REVERT: C 178 LYS cc_start: 0.7287 (mttm) cc_final: 0.6106 (mmpt) REVERT: C 180 ARG cc_start: 0.7696 (mtt180) cc_final: 0.6628 (tpm170) outliers start: 10 outliers final: 2 residues processed: 93 average time/residue: 1.4005 time to fit residues: 133.1803 Evaluate side-chains 81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 229 GLN C 229 GLN C 239 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.132832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.118145 restraints weight = 5171.281| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.07 r_work: 0.3890 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 3312 Z= 0.604 Angle : 0.826 6.766 4503 Z= 0.465 Chirality : 0.056 0.156 543 Planarity : 0.004 0.027 558 Dihedral : 6.771 22.314 447 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.97 % Allowed : 21.16 % Favored : 74.87 % 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: -4.56 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 239 PHE 0.007 0.002 PHE B 171 TYR 0.024 0.003 TYR A 132 ARG 0.001 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.353 Fit side-chains REVERT: B 124 LYS cc_start: 0.8658 (mtmt) cc_final: 0.7017 (mmpt) REVERT: B 140 ARG cc_start: 0.5643 (mtt180) cc_final: 0.4750 (ppt170) REVERT: B 178 LYS cc_start: 0.7134 (mttm) cc_final: 0.5702 (pptt) REVERT: B 180 ARG cc_start: 0.7866 (mtt180) cc_final: 0.6465 (pmt170) REVERT: B 249 GLN cc_start: 0.8326 (tt0) cc_final: 0.7898 (tm-30) REVERT: B 252 ASP cc_start: 0.8089 (t0) cc_final: 0.7600 (t0) REVERT: A 178 LYS cc_start: 0.6876 (mttm) cc_final: 0.6485 (mtpt) REVERT: A 180 ARG cc_start: 0.7799 (mtt180) cc_final: 0.6818 (ttt180) REVERT: A 249 GLN cc_start: 0.8283 (tt0) cc_final: 0.7828 (tm-30) REVERT: C 139 LYS cc_start: 0.7637 (ptpp) cc_final: 0.6955 (mmpt) REVERT: C 178 LYS cc_start: 0.7386 (mttm) cc_final: 0.6190 (mmpt) REVERT: C 180 ARG cc_start: 0.7716 (mtt180) cc_final: 0.6538 (tpm170) REVERT: C 249 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8170 (tp-100) outliers start: 15 outliers final: 6 residues processed: 88 average time/residue: 1.5365 time to fit residues: 138.1564 Evaluate side-chains 84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 249 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 182 ASN A 148 ASN C 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.140625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.125103 restraints weight = 4920.149| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.09 r_work: 0.4032 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3933 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3312 Z= 0.179 Angle : 0.633 9.588 4503 Z= 0.346 Chirality : 0.052 0.144 543 Planarity : 0.002 0.027 558 Dihedral : 5.946 21.472 447 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.23 % Allowed : 23.28 % Favored : 72.49 % 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: -4.16 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 239 PHE 0.005 0.001 PHE A 213 TYR 0.016 0.002 TYR C 211 ARG 0.001 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: B 124 LYS cc_start: 0.8673 (mtmt) cc_final: 0.7061 (mmpt) REVERT: B 140 ARG cc_start: 0.5194 (mtt180) cc_final: 0.4298 (ptm-80) REVERT: B 148 ASN cc_start: 0.7416 (m-40) cc_final: 0.6912 (t0) REVERT: B 180 ARG cc_start: 0.7863 (mtt180) cc_final: 0.6419 (pmt170) REVERT: B 205 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: B 206 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8200 (tm-30) REVERT: B 207 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8163 (mtp) REVERT: B 249 GLN cc_start: 0.8240 (tt0) cc_final: 0.7905 (tm-30) REVERT: B 252 ASP cc_start: 0.8077 (t0) cc_final: 0.7606 (t0) REVERT: A 180 ARG cc_start: 0.7755 (mtt180) cc_final: 0.6796 (ttt180) REVERT: A 192 MET cc_start: 0.8137 (mtt) cc_final: 0.7759 (mtt) REVERT: A 205 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: A 206 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8323 (tm-30) REVERT: C 148 ASN cc_start: 0.7556 (m-40) cc_final: 0.7300 (t0) REVERT: C 163 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7192 (mt-10) REVERT: C 178 LYS cc_start: 0.7311 (mttm) cc_final: 0.6187 (mmpt) REVERT: C 180 ARG cc_start: 0.7612 (mtt180) cc_final: 0.6520 (tpm170) outliers start: 16 outliers final: 5 residues processed: 91 average time/residue: 1.3104 time to fit residues: 122.2588 Evaluate side-chains 80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain C residue 143 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 9 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN A 182 ASN C 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.139770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.124013 restraints weight = 4910.702| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.08 r_work: 0.4003 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3312 Z= 0.223 Angle : 0.633 9.507 4503 Z= 0.350 Chirality : 0.052 0.144 543 Planarity : 0.002 0.025 558 Dihedral : 5.875 20.860 447 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.70 % Allowed : 24.87 % Favored : 71.43 % 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: -3.98 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 239 PHE 0.005 0.001 PHE A 213 TYR 0.014 0.002 TYR C 211 ARG 0.001 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: B 124 LYS cc_start: 0.8658 (mtmt) cc_final: 0.7082 (mmpt) REVERT: B 140 ARG cc_start: 0.5223 (mtt180) cc_final: 0.4312 (ptm-80) REVERT: B 180 ARG cc_start: 0.7858 (mtt180) cc_final: 0.6435 (pmt170) REVERT: B 249 GLN cc_start: 0.8151 (tt0) cc_final: 0.7916 (tm-30) REVERT: B 251 VAL cc_start: 0.9190 (OUTLIER) cc_final: 0.8659 (t) REVERT: B 252 ASP cc_start: 0.8075 (t0) cc_final: 0.7572 (t0) REVERT: A 180 ARG cc_start: 0.7780 (mtt180) cc_final: 0.6853 (ttt180) REVERT: A 192 MET cc_start: 0.8126 (mtt) cc_final: 0.7796 (mtt) REVERT: C 178 LYS cc_start: 0.7274 (mttm) cc_final: 0.6160 (mmpt) REVERT: C 180 ARG cc_start: 0.7679 (mtt180) cc_final: 0.6542 (tpm170) REVERT: C 247 ARG cc_start: 0.8945 (ttt-90) cc_final: 0.8723 (ttt90) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 1.3741 time to fit residues: 123.7463 Evaluate side-chains 84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 182 ASN A 148 ASN A 182 ASN C 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.138742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.122849 restraints weight = 5048.487| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.09 r_work: 0.3982 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3312 Z= 0.271 Angle : 0.664 9.078 4503 Z= 0.368 Chirality : 0.052 0.143 543 Planarity : 0.003 0.025 558 Dihedral : 5.944 21.161 447 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.23 % Allowed : 25.13 % Favored : 70.63 % 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: -3.91 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 239 PHE 0.007 0.001 PHE A 213 TYR 0.017 0.002 TYR B 143 ARG 0.001 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: B 124 LYS cc_start: 0.8637 (mtmt) cc_final: 0.7059 (mmpt) REVERT: B 140 ARG cc_start: 0.5253 (mtt180) cc_final: 0.4306 (ptm-80) REVERT: B 180 ARG cc_start: 0.7880 (mtt180) cc_final: 0.6462 (pmt170) REVERT: B 249 GLN cc_start: 0.8181 (tt0) cc_final: 0.7841 (tm-30) REVERT: B 251 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8667 (t) REVERT: B 252 ASP cc_start: 0.8071 (t0) cc_final: 0.7540 (t0) REVERT: A 180 ARG cc_start: 0.7801 (mtt180) cc_final: 0.6867 (ttt180) REVERT: A 192 MET cc_start: 0.8136 (mtt) cc_final: 0.7815 (mtt) REVERT: A 205 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: C 163 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7026 (mt-10) REVERT: C 178 LYS cc_start: 0.7272 (mttm) cc_final: 0.6164 (mmpt) REVERT: C 180 ARG cc_start: 0.7682 (mtt180) cc_final: 0.6538 (tpm170) outliers start: 16 outliers final: 10 residues processed: 87 average time/residue: 1.4010 time to fit residues: 124.6621 Evaluate side-chains 85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 0.0980 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.0040 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN A 182 ASN C 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.140411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.124525 restraints weight = 4824.460| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.07 r_work: 0.3999 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3312 Z= 0.224 Angle : 0.636 9.120 4503 Z= 0.354 Chirality : 0.051 0.140 543 Planarity : 0.002 0.025 558 Dihedral : 5.828 20.906 447 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.97 % Allowed : 26.19 % Favored : 69.84 % 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: -3.77 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.006 0.001 PHE A 213 TYR 0.013 0.002 TYR B 143 ARG 0.001 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 124 LYS cc_start: 0.8671 (mtmt) cc_final: 0.7093 (mmpt) REVERT: B 140 ARG cc_start: 0.5208 (mtt180) cc_final: 0.4260 (ptm-80) REVERT: B 180 ARG cc_start: 0.7868 (mtt180) cc_final: 0.6435 (pmt170) REVERT: B 251 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.8672 (t) REVERT: B 252 ASP cc_start: 0.8024 (t0) cc_final: 0.7469 (t0) REVERT: A 180 ARG cc_start: 0.7794 (mtt180) cc_final: 0.6879 (ttt180) REVERT: A 192 MET cc_start: 0.8116 (mtt) cc_final: 0.7798 (mtt) REVERT: A 205 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: C 139 LYS cc_start: 0.7199 (ptpp) cc_final: 0.6347 (mmpt) REVERT: C 163 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7011 (mt-10) REVERT: C 178 LYS cc_start: 0.7244 (mttm) cc_final: 0.6143 (mmpt) REVERT: C 180 ARG cc_start: 0.7661 (mtt180) cc_final: 0.6502 (tpm170) REVERT: C 247 ARG cc_start: 0.8955 (ttt-90) cc_final: 0.8728 (ttt90) REVERT: C 249 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8286 (tm-30) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 1.2814 time to fit residues: 114.2556 Evaluate side-chains 86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN A 148 ASN A 182 ASN C 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.139593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.123919 restraints weight = 4851.704| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.08 r_work: 0.3987 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3312 Z= 0.254 Angle : 0.664 9.145 4503 Z= 0.366 Chirality : 0.052 0.144 543 Planarity : 0.003 0.024 558 Dihedral : 5.856 20.914 447 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.70 % Allowed : 26.46 % Favored : 69.84 % 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: -3.70 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.004 0.001 PHE A 213 TYR 0.019 0.002 TYR B 143 ARG 0.001 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: B 124 LYS cc_start: 0.8669 (mtmt) cc_final: 0.7115 (mmpt) REVERT: B 140 ARG cc_start: 0.5172 (mtt180) cc_final: 0.4254 (ptm-80) REVERT: B 180 ARG cc_start: 0.7880 (mtt180) cc_final: 0.6472 (pmt170) REVERT: B 252 ASP cc_start: 0.8035 (t0) cc_final: 0.7705 (t0) REVERT: A 180 ARG cc_start: 0.7798 (mtt180) cc_final: 0.6902 (ttt180) REVERT: A 192 MET cc_start: 0.8128 (mtt) cc_final: 0.7837 (mtt) REVERT: A 205 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: C 139 LYS cc_start: 0.7179 (ptpp) cc_final: 0.6343 (mmpt) REVERT: C 178 LYS cc_start: 0.7258 (mttm) cc_final: 0.6164 (mmpt) REVERT: C 180 ARG cc_start: 0.7685 (mtt180) cc_final: 0.6539 (tpm170) REVERT: C 247 ARG cc_start: 0.8945 (ttt-90) cc_final: 0.8709 (ttt90) REVERT: C 249 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8274 (tm-30) outliers start: 14 outliers final: 8 residues processed: 85 average time/residue: 1.4752 time to fit residues: 128.3547 Evaluate side-chains 84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 182 ASN A 182 ASN C 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.141677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.126119 restraints weight = 4842.260| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.04 r_work: 0.4015 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3312 Z= 0.244 Angle : 0.663 9.511 4503 Z= 0.367 Chirality : 0.051 0.141 543 Planarity : 0.002 0.025 558 Dihedral : 5.832 20.663 447 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.91 % Allowed : 27.25 % Favored : 69.84 % 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: -3.66 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 239 PHE 0.004 0.001 PHE A 237 TYR 0.017 0.002 TYR B 143 ARG 0.001 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: B 124 LYS cc_start: 0.8675 (mtmt) cc_final: 0.7106 (mmpt) REVERT: B 140 ARG cc_start: 0.5186 (mtt180) cc_final: 0.4253 (ptm-80) REVERT: B 180 ARG cc_start: 0.7863 (mtt180) cc_final: 0.6469 (pmt170) REVERT: B 252 ASP cc_start: 0.7994 (t0) cc_final: 0.7589 (t0) REVERT: A 180 ARG cc_start: 0.7800 (mtt180) cc_final: 0.6915 (ttt180) REVERT: A 192 MET cc_start: 0.8132 (mtt) cc_final: 0.7852 (mtt) REVERT: A 205 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: C 139 LYS cc_start: 0.7165 (ptpp) cc_final: 0.6327 (mmpt) REVERT: C 178 LYS cc_start: 0.7252 (mttm) cc_final: 0.6157 (mmpt) REVERT: C 180 ARG cc_start: 0.7686 (mtt180) cc_final: 0.6550 (tpm170) REVERT: C 247 ARG cc_start: 0.8952 (ttt-90) cc_final: 0.8714 (ttt90) REVERT: C 249 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8244 (tm-30) outliers start: 11 outliers final: 9 residues processed: 82 average time/residue: 1.4123 time to fit residues: 118.4668 Evaluate side-chains 82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN A 148 ASN A 182 ASN C 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.148322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.132889 restraints weight = 4659.839| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.02 r_work: 0.4065 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3312 Z= 0.178 Angle : 0.634 9.517 4503 Z= 0.347 Chirality : 0.051 0.139 543 Planarity : 0.002 0.024 558 Dihedral : 5.599 19.422 447 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.91 % Allowed : 27.25 % Favored : 69.84 % 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: -3.54 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 239 PHE 0.005 0.001 PHE A 237 TYR 0.012 0.001 TYR B 143 ARG 0.001 0.000 ARG C 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.400 Fit side-chains REVERT: B 124 LYS cc_start: 0.8679 (mtmt) cc_final: 0.7128 (mmpt) REVERT: B 140 ARG cc_start: 0.5151 (mtt180) cc_final: 0.4210 (ptm-80) REVERT: B 180 ARG cc_start: 0.7830 (mtt180) cc_final: 0.6517 (pmt170) REVERT: B 252 ASP cc_start: 0.7982 (t0) cc_final: 0.7568 (t0) REVERT: A 180 ARG cc_start: 0.7755 (mtt180) cc_final: 0.6952 (ttt180) REVERT: A 192 MET cc_start: 0.8097 (mtt) cc_final: 0.7761 (mtt) REVERT: C 139 LYS cc_start: 0.7063 (ptpp) cc_final: 0.6148 (mmpt) REVERT: C 163 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6917 (mt-10) REVERT: C 178 LYS cc_start: 0.7258 (mttm) cc_final: 0.6154 (mmpt) REVERT: C 180 ARG cc_start: 0.7663 (mtt180) cc_final: 0.6621 (tpm170) REVERT: C 247 ARG cc_start: 0.8926 (ttt-90) cc_final: 0.8679 (ttt90) outliers start: 11 outliers final: 7 residues processed: 85 average time/residue: 1.2416 time to fit residues: 108.2140 Evaluate side-chains 79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 182 ASN A 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.146488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.130679 restraints weight = 4818.554| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.12 r_work: 0.4047 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3950 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3312 Z= 0.208 Angle : 0.656 9.797 4503 Z= 0.361 Chirality : 0.051 0.139 543 Planarity : 0.002 0.023 558 Dihedral : 5.616 18.935 447 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.38 % Allowed : 28.57 % Favored : 69.05 % 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: -3.45 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS A 239 PHE 0.006 0.001 PHE A 213 TYR 0.013 0.002 TYR B 143 ARG 0.001 0.000 ARG C 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3457.93 seconds wall clock time: 59 minutes 53.86 seconds (3593.86 seconds total)