Starting phenix.real_space_refine on Sun Mar 10 16:13:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x84_33055/03_2024/7x84_33055.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x84_33055/03_2024/7x84_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x84_33055/03_2024/7x84_33055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x84_33055/03_2024/7x84_33055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x84_33055/03_2024/7x84_33055.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x84_33055/03_2024/7x84_33055.pdb" } 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 Residue "B ARG 180": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} 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} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Time building chain proxies: 2.25, per 1000 atoms: 0.69 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=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.43 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: 0.71 Time building geometry restraints manager: 1.26 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: 99.43 - 105.78: 35 105.78 - 112.13: 1687 112.13 - 118.48: 934 118.48 - 124.83: 1826 124.83 - 131.18: 21 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: 1767 15.39 - 30.77: 157 30.77 - 46.16: 65 46.16 - 61.54: 3 61.54 - 76.93: 3 Dihedral angle restraints: 1995 sinusoidal: 777 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 1992 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: 2.26 - 2.79: 685 2.79 - 3.32: 2939 3.32 - 3.84: 5161 3.84 - 4.37: 5887 4.37 - 4.90: 11776 Nonbonded interactions: 26448 Sorted by model distance: nonbonded pdb=" O ASN A 148 " pdb=" OG1 THR A 149 " model vdw 2.259 2.440 nonbonded pdb=" O ASN C 148 " pdb=" OG1 THR C 149 " model vdw 2.259 2.440 nonbonded pdb=" O ASN B 148 " pdb=" OG1 THR B 149 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR C 236 " pdb=" O HIS C 239 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR A 236 " pdb=" O HIS A 239 " model vdw 2.263 2.440 ... (remaining 26443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 16.420 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 13.500 Find NCS groups from input model: 0.190 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.070 ------------------------------------------------------------------------------- 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= 0.521 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 : 2.259 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 fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.394 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: 1.3065 time to fit residues: 127.1268 Evaluate side-chains 75 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3312 Z= 0.234 Angle : 0.633 5.332 4503 Z= 0.359 Chirality : 0.052 0.145 543 Planarity : 0.002 0.021 558 Dihedral : 6.073 19.185 447 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.65 % Allowed : 19.31 % Favored : 78.04 % 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: -4.82 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 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 140 *********************** 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 95 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.436 Fit side-chains REVERT: B 124 LYS cc_start: 0.8594 (mtmt) cc_final: 0.7086 (mmpt) REVERT: B 140 ARG cc_start: 0.5404 (mtt180) cc_final: 0.4562 (ptm-80) REVERT: B 148 ASN cc_start: 0.7327 (m-40) cc_final: 0.7025 (t0) REVERT: B 178 LYS cc_start: 0.7106 (mttm) cc_final: 0.5824 (pptt) REVERT: B 180 ARG cc_start: 0.7461 (mtt180) cc_final: 0.6398 (pmt170) REVERT: B 190 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7974 (tt) REVERT: B 206 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8210 (tm-30) REVERT: B 252 ASP cc_start: 0.7660 (t0) cc_final: 0.7249 (t0) REVERT: A 178 LYS cc_start: 0.6947 (mttm) cc_final: 0.6554 (mtpt) REVERT: A 180 ARG cc_start: 0.7440 (mtt180) cc_final: 0.6870 (ttt90) REVERT: A 205 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: C 178 LYS cc_start: 0.7309 (mttm) cc_final: 0.6254 (mmpt) REVERT: C 180 ARG cc_start: 0.7378 (mtt180) cc_final: 0.6626 (tpm170) outliers start: 10 outliers final: 3 residues processed: 89 average time/residue: 1.3871 time to fit residues: 126.2728 Evaluate side-chains 84 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 19 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1821 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= 0.279 Angle : 0.654 6.902 4503 Z= 0.364 Chirality : 0.052 0.148 543 Planarity : 0.002 0.022 558 Dihedral : 5.975 20.666 447 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.70 % Allowed : 20.63 % Favored : 75.66 % 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: -4.31 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.005 0.001 PHE A 213 TYR 0.014 0.002 TYR A 132 ARG 0.001 0.000 ARG C 140 *********************** 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 fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.401 Fit side-chains REVERT: B 124 LYS cc_start: 0.8567 (mtmt) cc_final: 0.7079 (mmpt) REVERT: B 140 ARG cc_start: 0.5393 (mtt180) cc_final: 0.4558 (ptm-80) REVERT: B 178 LYS cc_start: 0.7120 (mttm) cc_final: 0.5827 (pptt) REVERT: B 180 ARG cc_start: 0.7490 (mtt180) cc_final: 0.6419 (pmt170) REVERT: B 252 ASP cc_start: 0.7620 (t0) cc_final: 0.7282 (t0) REVERT: A 148 ASN cc_start: 0.6779 (t0) cc_final: 0.6245 (m-40) REVERT: A 178 LYS cc_start: 0.6957 (mttm) cc_final: 0.6572 (mtpt) REVERT: A 180 ARG cc_start: 0.7442 (mtt180) cc_final: 0.6849 (ttt90) REVERT: A 249 GLN cc_start: 0.8055 (tp40) cc_final: 0.7822 (tm-30) REVERT: C 178 LYS cc_start: 0.7286 (mttm) cc_final: 0.6250 (mmpt) REVERT: C 180 ARG cc_start: 0.7372 (mtt180) cc_final: 0.6603 (tpm170) REVERT: C 249 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7868 (tm-30) outliers start: 14 outliers final: 3 residues processed: 87 average time/residue: 1.3826 time to fit residues: 123.1046 Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B 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 18 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN C 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3312 Z= 0.464 Angle : 0.757 10.302 4503 Z= 0.419 Chirality : 0.053 0.164 543 Planarity : 0.003 0.025 558 Dihedral : 6.356 24.022 447 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 4.76 % Allowed : 22.49 % Favored : 72.75 % 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: -4.24 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 239 PHE 0.006 0.001 PHE B 171 TYR 0.020 0.003 TYR A 132 ARG 0.001 0.000 ARG B 180 *********************** 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 93 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.393 Fit side-chains REVERT: B 124 LYS cc_start: 0.8553 (mtmt) cc_final: 0.7046 (mmpt) REVERT: B 140 ARG cc_start: 0.5630 (mtt180) cc_final: 0.4846 (ptm-80) REVERT: B 178 LYS cc_start: 0.7178 (mttm) cc_final: 0.5820 (pptt) REVERT: B 180 ARG cc_start: 0.7454 (mtt180) cc_final: 0.6417 (pmt170) REVERT: B 205 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: B 246 GLU cc_start: 0.8522 (pt0) cc_final: 0.8182 (pt0) REVERT: B 252 ASP cc_start: 0.7656 (t0) cc_final: 0.7277 (t0) REVERT: A 178 LYS cc_start: 0.6987 (mttm) cc_final: 0.6585 (mtpt) REVERT: A 180 ARG cc_start: 0.7477 (mtt180) cc_final: 0.6898 (ttt180) REVERT: A 249 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: C 178 LYS cc_start: 0.7324 (mttm) cc_final: 0.6266 (mmpt) REVERT: C 180 ARG cc_start: 0.7403 (mtt180) cc_final: 0.6520 (tpm170) REVERT: C 249 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7668 (tp-100) outliers start: 18 outliers final: 8 residues processed: 85 average time/residue: 1.4181 time to fit residues: 123.3062 Evaluate side-chains 85 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 205 GLU 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 228 MET Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 249 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3312 Z= 0.190 Angle : 0.617 9.153 4503 Z= 0.340 Chirality : 0.051 0.143 543 Planarity : 0.002 0.025 558 Dihedral : 5.825 24.315 447 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % 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: -3.94 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.27), 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 237 TYR 0.010 0.002 TYR A 132 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 91 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: B 124 LYS cc_start: 0.8565 (mtmt) cc_final: 0.7099 (mmpt) REVERT: B 140 ARG cc_start: 0.5490 (mtt180) cc_final: 0.4659 (ptm-80) REVERT: B 180 ARG cc_start: 0.7453 (mtt180) cc_final: 0.6394 (pmt170) REVERT: B 205 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: B 246 GLU cc_start: 0.8282 (pt0) cc_final: 0.7923 (pt0) REVERT: B 252 ASP cc_start: 0.7506 (t0) cc_final: 0.7261 (t0) REVERT: A 180 ARG cc_start: 0.7421 (mtt180) cc_final: 0.6846 (ttt180) REVERT: A 205 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: C 124 LYS cc_start: 0.8525 (mttp) cc_final: 0.8313 (mttp) REVERT: C 148 ASN cc_start: 0.7650 (m-40) cc_final: 0.7438 (t0) REVERT: C 178 LYS cc_start: 0.7254 (mttm) cc_final: 0.6268 (mmpt) REVERT: C 180 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6542 (tpm170) outliers start: 15 outliers final: 7 residues processed: 86 average time/residue: 1.3772 time to fit residues: 121.1856 Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 205 GLU 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 137 VAL 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 9 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3312 Z= 0.155 Angle : 0.583 8.263 4503 Z= 0.323 Chirality : 0.051 0.142 543 Planarity : 0.002 0.024 558 Dihedral : 5.569 24.187 447 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.97 % Allowed : 26.46 % Favored : 69.58 % 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: -3.67 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.27), 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 237 TYR 0.011 0.001 TYR A 135 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 95 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.376 Fit side-chains REVERT: B 124 LYS cc_start: 0.8594 (mtmt) cc_final: 0.7103 (mmpt) REVERT: B 140 ARG cc_start: 0.5460 (mtt180) cc_final: 0.4606 (ptm-80) REVERT: B 180 ARG cc_start: 0.7476 (mtt180) cc_final: 0.6386 (pmt170) REVERT: B 246 GLU cc_start: 0.8192 (pt0) cc_final: 0.7888 (pt0) REVERT: B 249 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7931 (tm-30) REVERT: B 252 ASP cc_start: 0.7498 (t0) cc_final: 0.7059 (t0) REVERT: A 129 LYS cc_start: 0.7844 (ptpt) cc_final: 0.7597 (ptmt) REVERT: A 180 ARG cc_start: 0.7415 (mtt180) cc_final: 0.6857 (ttt180) REVERT: A 205 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: C 139 LYS cc_start: 0.7086 (ptpp) cc_final: 0.6310 (mmpt) REVERT: C 148 ASN cc_start: 0.7638 (m-40) cc_final: 0.7382 (t0) REVERT: C 163 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: C 178 LYS cc_start: 0.7247 (mttm) cc_final: 0.6217 (mmpt) REVERT: C 180 ARG cc_start: 0.7340 (mtt180) cc_final: 0.6559 (tpm170) REVERT: C 247 ARG cc_start: 0.8555 (ttt-90) cc_final: 0.8355 (ttt90) outliers start: 15 outliers final: 4 residues processed: 89 average time/residue: 1.4033 time to fit residues: 127.8477 Evaluate side-chains 75 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 153 THR 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 163 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.0170 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 1.4022 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3312 Z= 0.201 Angle : 0.631 7.996 4503 Z= 0.345 Chirality : 0.051 0.144 543 Planarity : 0.002 0.024 558 Dihedral : 5.605 22.604 447 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.70 % Allowed : 27.25 % 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: -3.63 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.005 0.001 PHE A 213 TYR 0.016 0.002 TYR C 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 85 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.415 Fit side-chains REVERT: B 124 LYS cc_start: 0.8587 (mtmt) cc_final: 0.7127 (mmpt) REVERT: B 140 ARG cc_start: 0.5438 (mtt180) cc_final: 0.4631 (ptm-80) REVERT: B 180 ARG cc_start: 0.7411 (mtt180) cc_final: 0.6379 (pmt170) REVERT: B 246 GLU cc_start: 0.8194 (pt0) cc_final: 0.7888 (pt0) REVERT: A 129 LYS cc_start: 0.7878 (ptpt) cc_final: 0.7638 (ptmt) REVERT: A 180 ARG cc_start: 0.7424 (mtt180) cc_final: 0.6879 (ttt180) REVERT: A 205 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: C 124 LYS cc_start: 0.8540 (mttp) cc_final: 0.8327 (mttp) REVERT: C 148 ASN cc_start: 0.7629 (m-40) cc_final: 0.7344 (t0) REVERT: C 178 LYS cc_start: 0.7209 (mttm) cc_final: 0.6181 (mmpt) REVERT: C 180 ARG cc_start: 0.7345 (mtt180) cc_final: 0.6520 (tpm170) REVERT: C 247 ARG cc_start: 0.8564 (ttt-90) cc_final: 0.8280 (ttt90) outliers start: 14 outliers final: 6 residues processed: 81 average time/residue: 1.3386 time to fit residues: 111.0578 Evaluate side-chains 78 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain C residue 136 ASP 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 3 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3312 Z= 0.329 Angle : 0.710 8.190 4503 Z= 0.386 Chirality : 0.052 0.209 543 Planarity : 0.003 0.025 558 Dihedral : 5.949 23.406 447 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.50 % Allowed : 26.46 % 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: -3.66 (0.36), 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 0.006 0.002 HIS C 239 PHE 0.005 0.001 PHE A 213 TYR 0.020 0.002 TYR C 143 ARG 0.001 0.000 ARG A 140 *********************** 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 92 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: B 124 LYS cc_start: 0.8548 (mtmt) cc_final: 0.7081 (mmpt) REVERT: B 140 ARG cc_start: 0.5615 (mtt180) cc_final: 0.4795 (ptm-80) REVERT: B 180 ARG cc_start: 0.7444 (mtt180) cc_final: 0.6411 (pmt170) REVERT: B 246 GLU cc_start: 0.8336 (pt0) cc_final: 0.8011 (pt0) REVERT: A 143 TYR cc_start: 0.6458 (OUTLIER) cc_final: 0.5017 (m-80) REVERT: A 180 ARG cc_start: 0.7452 (mtt180) cc_final: 0.6908 (ttt180) REVERT: A 205 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: C 178 LYS cc_start: 0.7216 (mttm) cc_final: 0.6173 (mmpt) REVERT: C 180 ARG cc_start: 0.7401 (mtt180) cc_final: 0.6535 (tpm170) REVERT: C 247 ARG cc_start: 0.8570 (ttt-90) cc_final: 0.8305 (ttt90) outliers start: 17 outliers final: 8 residues processed: 85 average time/residue: 1.3599 time to fit residues: 118.2808 Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 149 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 153 THR 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 33 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3312 Z= 0.235 Angle : 0.687 11.651 4503 Z= 0.368 Chirality : 0.051 0.145 543 Planarity : 0.002 0.024 558 Dihedral : 5.813 23.520 447 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.17 % Allowed : 28.31 % Favored : 68.52 % 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: -3.64 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.005 0.001 PHE A 213 TYR 0.015 0.002 TYR C 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 82 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: B 124 LYS cc_start: 0.8569 (mtmt) cc_final: 0.7104 (mmpt) REVERT: B 140 ARG cc_start: 0.5637 (mtt180) cc_final: 0.4782 (ptm-80) REVERT: B 180 ARG cc_start: 0.7419 (mtt180) cc_final: 0.6402 (pmt170) REVERT: B 246 GLU cc_start: 0.8281 (pt0) cc_final: 0.7930 (pt0) REVERT: A 180 ARG cc_start: 0.7427 (mtt180) cc_final: 0.6894 (ttt180) REVERT: A 192 MET cc_start: 0.7952 (mtt) cc_final: 0.7353 (mtt) REVERT: C 178 LYS cc_start: 0.7213 (mttm) cc_final: 0.6203 (mmpt) REVERT: C 180 ARG cc_start: 0.7352 (mtt180) cc_final: 0.6519 (tpm170) REVERT: C 247 ARG cc_start: 0.8563 (ttt-90) cc_final: 0.8289 (ttt90) outliers start: 12 outliers final: 8 residues processed: 79 average time/residue: 1.4868 time to fit residues: 120.1305 Evaluate side-chains 78 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 153 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3312 Z= 0.352 Angle : 0.736 10.398 4503 Z= 0.398 Chirality : 0.052 0.153 543 Planarity : 0.003 0.025 558 Dihedral : 6.022 23.618 447 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.17 % Allowed : 28.31 % Favored : 68.52 % 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 0.006 0.002 HIS C 239 PHE 0.006 0.001 PHE B 171 TYR 0.019 0.002 TYR C 143 ARG 0.001 0.000 ARG B 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 83 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: B 124 LYS cc_start: 0.8548 (mtmt) cc_final: 0.7089 (mmpt) REVERT: B 140 ARG cc_start: 0.5694 (mtt180) cc_final: 0.4872 (tmm160) REVERT: B 180 ARG cc_start: 0.7450 (mtt180) cc_final: 0.6422 (pmt170) REVERT: B 249 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7582 (tp40) REVERT: A 180 ARG cc_start: 0.7456 (mtt180) cc_final: 0.6916 (ttt180) REVERT: A 192 MET cc_start: 0.8009 (mtt) cc_final: 0.7514 (mtt) REVERT: C 178 LYS cc_start: 0.7236 (mttm) cc_final: 0.6231 (mmpt) REVERT: C 180 ARG cc_start: 0.7376 (mtt180) cc_final: 0.6519 (tpm170) REVERT: C 247 ARG cc_start: 0.8574 (ttt-90) cc_final: 0.8305 (ttt90) REVERT: C 249 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7637 (tp-100) outliers start: 12 outliers final: 6 residues processed: 78 average time/residue: 1.4389 time to fit residues: 114.8100 Evaluate side-chains 78 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 249 GLN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 249 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.138336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.123345 restraints weight = 5063.383| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.05 r_work: 0.3962 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3312 Z= 0.373 Angle : 0.757 10.743 4503 Z= 0.411 Chirality : 0.053 0.191 543 Planarity : 0.003 0.025 558 Dihedral : 6.155 24.322 447 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.17 % Allowed : 28.84 % Favored : 67.99 % 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 : -2.87 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.006 0.001 PHE B 171 TYR 0.020 0.002 TYR C 143 ARG 0.001 0.000 ARG B 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.96 seconds wall clock time: 44 minutes 53.54 seconds (2693.54 seconds total)