Starting phenix.real_space_refine on Sun Mar 10 20:39:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/03_2024/7f73_31484.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/03_2024/7f73_31484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/03_2024/7f73_31484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/03_2024/7f73_31484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/03_2024/7f73_31484.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f73_31484/03_2024/7f73_31484.pdb" } resolution = 4.0 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= 0.007 sd= 0.086 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 22 5.16 5 C 3248 2.51 5 N 816 2.21 5 O 848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ARG 10": "NH1" <-> "NH2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "B ARG 10": "NH1" <-> "NH2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B ARG 299": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4934 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2467 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 4, 'TRANS': 288} Chain breaks: 1 Chain: "B" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2467 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 4, 'TRANS': 288} Chain breaks: 1 Time building chain proxies: 3.27, per 1000 atoms: 0.66 Number of scatterers: 4934 At special positions: 0 Unit cell: (83.699, 118.483, 94.569, 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 22 16.00 O 848 8.00 N 816 7.00 C 3248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 1.83 Conformation dependent library (CDL) restraints added in 828.3 milliseconds 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 87.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 5 through 64 Processing helix chain 'A' and resid 69 through 97 Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 118 through 150 removed outlier: 4.338A pdb=" N ALA A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 182 removed outlier: 3.724A pdb=" N ASP A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 205 removed outlier: 4.608A pdb=" N SER A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 235 removed outlier: 3.549A pdb=" N GLN A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASN A 217 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 296 removed outlier: 3.948A pdb=" N SER A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 329 removed outlier: 3.567A pdb=" N PHE A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 64 Processing helix chain 'B' and resid 69 through 97 Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 118 through 150 removed outlier: 4.338A pdb=" N ALA B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 182 removed outlier: 3.724A pdb=" N ASP B 157 " --> pdb=" O TYR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 205 removed outlier: 4.608A pdb=" N SER B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 235 removed outlier: 3.549A pdb=" N GLN B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASN B 217 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 296 removed outlier: 3.948A pdb=" N SER B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 329 removed outlier: 3.566A pdb=" N PHE B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1233 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: 1.40 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1078 1.33 - 1.45: 1216 1.45 - 1.57: 2742 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 5064 Sorted by residual: bond pdb=" N THR B 205 " pdb=" CA THR B 205 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.10e-02 8.26e+03 1.11e+01 bond pdb=" N THR A 205 " pdb=" CA THR A 205 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.10e-02 8.26e+03 1.10e+01 bond pdb=" N VAL A 202 " pdb=" CA VAL A 202 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.05e+00 bond pdb=" N VAL B 202 " pdb=" CA VAL B 202 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.70e+00 bond pdb=" N PHE A 149 " pdb=" CA PHE A 149 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.27e-02 6.20e+03 8.22e+00 ... (remaining 5059 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.93: 94 106.93 - 113.76: 2723 113.76 - 120.58: 2329 120.58 - 127.41: 1644 127.41 - 134.24: 54 Bond angle restraints: 6844 Sorted by residual: angle pdb=" C PHE A 149 " pdb=" N VAL A 150 " pdb=" CA VAL A 150 " ideal model delta sigma weight residual 122.97 117.47 5.50 9.80e-01 1.04e+00 3.14e+01 angle pdb=" C PHE B 149 " pdb=" N VAL B 150 " pdb=" CA VAL B 150 " ideal model delta sigma weight residual 122.97 117.51 5.46 9.80e-01 1.04e+00 3.11e+01 angle pdb=" CA GLN B 78 " pdb=" CB GLN B 78 " pdb=" CG GLN B 78 " ideal model delta sigma weight residual 114.10 124.10 -10.00 2.00e+00 2.50e-01 2.50e+01 angle pdb=" CA GLN A 78 " pdb=" CB GLN A 78 " pdb=" CG GLN A 78 " ideal model delta sigma weight residual 114.10 124.09 -9.99 2.00e+00 2.50e-01 2.49e+01 angle pdb=" N PHE B 149 " pdb=" CA PHE B 149 " pdb=" C PHE B 149 " ideal model delta sigma weight residual 113.41 118.88 -5.47 1.22e+00 6.72e-01 2.01e+01 ... (remaining 6839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 2566 17.01 - 34.02: 300 34.02 - 51.03: 68 51.03 - 68.04: 15 68.04 - 85.05: 3 Dihedral angle restraints: 2952 sinusoidal: 1208 harmonic: 1744 Sorted by residual: dihedral pdb=" CA TRP B 188 " pdb=" C TRP B 188 " pdb=" N TRP B 189 " pdb=" CA TRP B 189 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA TRP A 188 " pdb=" C TRP A 188 " pdb=" N TRP A 189 " pdb=" CA TRP A 189 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ARG B 299 " pdb=" C ARG B 299 " pdb=" N GLU B 300 " pdb=" CA GLU B 300 " ideal model delta harmonic sigma weight residual 180.00 164.35 15.65 0 5.00e+00 4.00e-02 9.79e+00 ... (remaining 2949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 516 0.049 - 0.099: 147 0.099 - 0.148: 55 0.148 - 0.197: 25 0.197 - 0.246: 5 Chirality restraints: 748 Sorted by residual: chirality pdb=" CA MET A 203 " pdb=" N MET A 203 " pdb=" C MET A 203 " pdb=" CB MET A 203 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA MET B 203 " pdb=" N MET B 203 " pdb=" C MET B 203 " pdb=" CB MET B 203 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA TYR A 96 " pdb=" N TYR A 96 " pdb=" C TYR A 96 " pdb=" CB TYR A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 745 not shown) Planarity restraints: 844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 206 " -0.008 2.00e-02 2.50e+03 1.31e-02 4.31e+00 pdb=" CG TRP B 206 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP B 206 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 206 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 206 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 206 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 206 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 206 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 206 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 206 " -0.008 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP A 206 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 206 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 206 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 206 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 206 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 206 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 206 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 206 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 90 " 0.010 2.00e-02 2.50e+03 1.49e-02 3.89e+00 pdb=" CG PHE B 90 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 90 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 90 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 90 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 90 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 90 " -0.001 2.00e-02 2.50e+03 ... (remaining 841 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1010 2.78 - 3.31: 5029 3.31 - 3.84: 7936 3.84 - 4.37: 8858 4.37 - 4.90: 14744 Nonbonded interactions: 37577 Sorted by model distance: nonbonded pdb=" OE1 GLN A 230 " pdb=" OE1 GLN A 233 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLN B 230 " pdb=" OE1 GLN B 233 " model vdw 2.247 3.040 nonbonded pdb=" NE ARG A 86 " pdb=" CZ PHE A 90 " model vdw 2.290 3.420 nonbonded pdb=" NE ARG B 86 " pdb=" CZ PHE B 90 " model vdw 2.290 3.420 nonbonded pdb=" O LYS A 49 " pdb=" ND1 HIS A 53 " model vdw 2.303 2.520 ... (remaining 37572 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 2.500 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.450 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 : 0.007 0.045 5064 Z= 0.415 Angle : 1.070 10.003 6844 Z= 0.679 Chirality : 0.061 0.246 748 Planarity : 0.005 0.027 844 Dihedral : 15.265 85.051 1820 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.10 % Allowed : 0.37 % Favored : 95.52 % 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: 0.17 (0.32), residues: 578 helix: 0.32 (0.22), residues: 476 sheet: None (None), residues: 0 loop : -0.25 (0.51), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 206 HIS 0.013 0.002 HIS B 192 PHE 0.034 0.002 PHE B 90 TYR 0.011 0.002 TYR A 125 ARG 0.003 0.001 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7986 (t0) cc_final: 0.7583 (p0) REVERT: A 130 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: A 149 PHE cc_start: 0.5287 (OUTLIER) cc_final: 0.4865 (m-80) REVERT: B 149 PHE cc_start: 0.5172 (OUTLIER) cc_final: 0.4686 (m-80) outliers start: 22 outliers final: 8 residues processed: 121 average time/residue: 0.2012 time to fit residues: 29.9269 Evaluate side-chains 76 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN B 78 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5064 Z= 0.186 Angle : 0.622 7.441 6844 Z= 0.332 Chirality : 0.037 0.165 748 Planarity : 0.004 0.025 844 Dihedral : 8.490 58.432 659 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.92 % Allowed : 9.70 % Favored : 86.38 % 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: 2.07 (0.34), residues: 578 helix: 1.81 (0.23), residues: 476 sheet: None (None), residues: 0 loop : -0.66 (0.58), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 206 HIS 0.007 0.001 HIS A 53 PHE 0.015 0.001 PHE B 290 TYR 0.013 0.002 TYR A 236 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8175 (t0) cc_final: 0.7517 (p0) REVERT: A 142 LEU cc_start: 0.7935 (tp) cc_final: 0.7725 (tp) REVERT: A 149 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.5377 (m-80) REVERT: A 234 TYR cc_start: 0.7597 (t80) cc_final: 0.7304 (t80) REVERT: B 149 PHE cc_start: 0.5953 (OUTLIER) cc_final: 0.5346 (m-80) REVERT: B 203 MET cc_start: 0.8048 (mmm) cc_final: 0.7684 (tpp) outliers start: 21 outliers final: 11 residues processed: 93 average time/residue: 0.1644 time to fit residues: 19.7168 Evaluate side-chains 77 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 50 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5064 Z= 0.191 Angle : 0.627 11.172 6844 Z= 0.330 Chirality : 0.038 0.157 748 Planarity : 0.004 0.024 844 Dihedral : 6.511 54.499 648 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.54 % Allowed : 15.86 % Favored : 80.60 % 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: 2.57 (0.34), residues: 578 helix: 2.15 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -0.69 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 12 HIS 0.008 0.001 HIS A 53 PHE 0.031 0.002 PHE A 91 TYR 0.020 0.001 TYR A 29 ARG 0.005 0.000 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8280 (t0) cc_final: 0.7397 (p0) REVERT: A 142 LEU cc_start: 0.7927 (tp) cc_final: 0.7703 (tp) REVERT: A 149 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.5675 (m-80) REVERT: B 111 ASN cc_start: 0.8093 (t0) cc_final: 0.6779 (p0) REVERT: B 140 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7256 (mp) REVERT: B 149 PHE cc_start: 0.6172 (OUTLIER) cc_final: 0.5549 (m-80) REVERT: B 203 MET cc_start: 0.7800 (mmm) cc_final: 0.7379 (tpp) outliers start: 19 outliers final: 12 residues processed: 91 average time/residue: 0.1563 time to fit residues: 18.4477 Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 305 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5064 Z= 0.206 Angle : 0.658 11.019 6844 Z= 0.340 Chirality : 0.039 0.168 748 Planarity : 0.003 0.025 844 Dihedral : 6.188 54.452 648 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.48 % Allowed : 17.91 % Favored : 77.61 % 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: 2.56 (0.34), residues: 578 helix: 2.07 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -0.57 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 206 HIS 0.009 0.001 HIS A 13 PHE 0.013 0.001 PHE A 90 TYR 0.009 0.001 TYR A 29 ARG 0.006 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8299 (t0) cc_final: 0.7299 (p0) REVERT: A 142 LEU cc_start: 0.7966 (tp) cc_final: 0.7754 (tp) REVERT: A 149 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.5719 (m-80) REVERT: B 27 ARG cc_start: 0.7913 (ptt90) cc_final: 0.7537 (ptt90) REVERT: B 111 ASN cc_start: 0.8127 (t0) cc_final: 0.6937 (p0) REVERT: B 149 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.5774 (m-80) REVERT: B 203 MET cc_start: 0.7857 (mmm) cc_final: 0.7344 (tpp) outliers start: 24 outliers final: 13 residues processed: 101 average time/residue: 0.1490 time to fit residues: 19.7940 Evaluate side-chains 90 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5064 Z= 0.306 Angle : 0.783 11.657 6844 Z= 0.403 Chirality : 0.044 0.216 748 Planarity : 0.004 0.028 844 Dihedral : 5.571 53.460 643 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.10 % Allowed : 22.20 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.34), residues: 578 helix: 1.71 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -1.47 (0.63), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 206 HIS 0.012 0.002 HIS B 13 PHE 0.043 0.002 PHE A 90 TYR 0.013 0.002 TYR A 29 ARG 0.006 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8315 (t0) cc_final: 0.7263 (p0) REVERT: A 142 LEU cc_start: 0.8017 (tp) cc_final: 0.7782 (tp) REVERT: A 149 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.5385 (m-80) REVERT: A 290 PHE cc_start: 0.6399 (t80) cc_final: 0.6175 (t80) REVERT: B 27 ARG cc_start: 0.7986 (ptt90) cc_final: 0.7742 (ptt90) REVERT: B 111 ASN cc_start: 0.8151 (t0) cc_final: 0.7057 (p0) REVERT: B 149 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.5935 (m-80) REVERT: B 203 MET cc_start: 0.8139 (mmm) cc_final: 0.7821 (tpp) outliers start: 22 outliers final: 16 residues processed: 94 average time/residue: 0.1502 time to fit residues: 18.7048 Evaluate side-chains 90 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.0270 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN B 78 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5064 Z= 0.169 Angle : 0.665 10.195 6844 Z= 0.343 Chirality : 0.039 0.195 748 Planarity : 0.003 0.023 844 Dihedral : 5.309 55.721 643 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.29 % Allowed : 23.13 % Favored : 72.57 % 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: 2.50 (0.34), residues: 578 helix: 2.11 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -1.50 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.012 0.002 HIS A 13 PHE 0.016 0.001 PHE B 90 TYR 0.025 0.001 TYR A 29 ARG 0.003 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8313 (t0) cc_final: 0.7153 (p0) REVERT: A 142 LEU cc_start: 0.7900 (tp) cc_final: 0.7626 (tp) REVERT: A 149 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.5679 (m-80) REVERT: A 234 TYR cc_start: 0.7700 (t80) cc_final: 0.7418 (t80) REVERT: A 235 TYR cc_start: 0.7292 (t80) cc_final: 0.7013 (t80) REVERT: B 96 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6553 (t80) REVERT: B 111 ASN cc_start: 0.8215 (t0) cc_final: 0.7047 (p0) REVERT: B 149 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.5737 (m-80) REVERT: B 203 MET cc_start: 0.8036 (mmm) cc_final: 0.7773 (tpp) outliers start: 23 outliers final: 11 residues processed: 93 average time/residue: 0.1441 time to fit residues: 17.8415 Evaluate side-chains 80 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 35 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5064 Z= 0.176 Angle : 0.701 11.724 6844 Z= 0.366 Chirality : 0.040 0.217 748 Planarity : 0.003 0.026 844 Dihedral : 5.257 57.092 643 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.54 % Allowed : 24.25 % Favored : 72.20 % 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: 2.54 (0.34), residues: 578 helix: 2.14 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -1.49 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.015 0.002 HIS B 13 PHE 0.059 0.002 PHE A 91 TYR 0.012 0.001 TYR A 29 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8246 (t0) cc_final: 0.7100 (p0) REVERT: A 142 LEU cc_start: 0.7914 (tp) cc_final: 0.7616 (tp) REVERT: A 149 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5718 (m-80) REVERT: A 234 TYR cc_start: 0.7676 (t80) cc_final: 0.7374 (t80) REVERT: A 235 TYR cc_start: 0.7218 (t80) cc_final: 0.6954 (t80) REVERT: A 277 CYS cc_start: 0.6611 (m) cc_final: 0.6190 (t) REVERT: B 111 ASN cc_start: 0.8195 (t0) cc_final: 0.6979 (p0) REVERT: B 140 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7420 (mp) REVERT: B 149 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.5607 (m-80) REVERT: B 203 MET cc_start: 0.7961 (mmm) cc_final: 0.7752 (tpp) outliers start: 19 outliers final: 13 residues processed: 87 average time/residue: 0.1443 time to fit residues: 17.2837 Evaluate side-chains 82 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5064 Z= 0.189 Angle : 0.693 12.653 6844 Z= 0.365 Chirality : 0.040 0.228 748 Planarity : 0.003 0.023 844 Dihedral : 5.288 58.414 643 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.66 % Allowed : 23.88 % Favored : 71.46 % 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: 2.56 (0.34), residues: 578 helix: 2.15 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.56 (0.62), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.011 0.002 HIS B 279 PHE 0.054 0.002 PHE A 91 TYR 0.025 0.001 TYR A 29 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 68 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 96 TYR cc_start: 0.6563 (t80) cc_final: 0.6308 (t80) REVERT: A 111 ASN cc_start: 0.8239 (t0) cc_final: 0.7069 (p0) REVERT: A 149 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5770 (m-80) REVERT: A 234 TYR cc_start: 0.7597 (t80) cc_final: 0.7234 (t80) REVERT: A 277 CYS cc_start: 0.6620 (m) cc_final: 0.6149 (t) REVERT: B 13 HIS cc_start: 0.8076 (m-70) cc_final: 0.7857 (p-80) REVERT: B 111 ASN cc_start: 0.8205 (t0) cc_final: 0.6975 (p0) REVERT: B 140 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7430 (mp) REVERT: B 149 PHE cc_start: 0.6488 (OUTLIER) cc_final: 0.5548 (m-80) REVERT: B 203 MET cc_start: 0.7911 (mmm) cc_final: 0.7565 (tpp) REVERT: B 290 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.5654 (t80) outliers start: 25 outliers final: 16 residues processed: 89 average time/residue: 0.1402 time to fit residues: 17.1005 Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5064 Z= 0.239 Angle : 0.775 15.228 6844 Z= 0.404 Chirality : 0.042 0.256 748 Planarity : 0.004 0.027 844 Dihedral : 5.402 59.137 643 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.85 % Allowed : 24.25 % Favored : 70.90 % 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: 2.35 (0.34), residues: 578 helix: 2.00 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -1.57 (0.62), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.010 0.002 HIS B 279 PHE 0.032 0.002 PHE A 90 TYR 0.016 0.001 TYR A 29 ARG 0.004 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 67 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 111 ASN cc_start: 0.8249 (t0) cc_final: 0.7032 (p0) REVERT: A 149 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.5771 (m-80) REVERT: A 234 TYR cc_start: 0.7601 (t80) cc_final: 0.7291 (t80) REVERT: A 235 TYR cc_start: 0.7362 (t80) cc_final: 0.7138 (t80) REVERT: B 96 TYR cc_start: 0.6964 (t80) cc_final: 0.6756 (t80) REVERT: B 111 ASN cc_start: 0.8235 (t0) cc_final: 0.7000 (p0) REVERT: B 140 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7562 (mp) REVERT: B 149 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.5507 (m-80) REVERT: B 203 MET cc_start: 0.7883 (mmm) cc_final: 0.7527 (tpp) outliers start: 26 outliers final: 20 residues processed: 89 average time/residue: 0.1321 time to fit residues: 16.1290 Evaluate side-chains 89 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN B 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5064 Z= 0.186 Angle : 0.741 15.611 6844 Z= 0.374 Chirality : 0.040 0.245 748 Planarity : 0.003 0.028 844 Dihedral : 5.260 58.562 643 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.29 % Allowed : 24.63 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.34), residues: 578 helix: 2.13 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -1.64 (0.60), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.010 0.002 HIS B 279 PHE 0.021 0.001 PHE B 90 TYR 0.031 0.001 TYR B 234 ARG 0.004 0.000 ARG B 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 13 HIS cc_start: 0.8086 (m90) cc_final: 0.7572 (p90) REVERT: A 96 TYR cc_start: 0.6363 (t80) cc_final: 0.6101 (t80) REVERT: A 111 ASN cc_start: 0.8193 (t0) cc_final: 0.6942 (p0) REVERT: A 123 PHE cc_start: 0.7306 (t80) cc_final: 0.7061 (t80) REVERT: A 149 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.5789 (m-80) REVERT: A 234 TYR cc_start: 0.7697 (t80) cc_final: 0.7411 (t80) REVERT: A 277 CYS cc_start: 0.6610 (m) cc_final: 0.6101 (t) REVERT: B 111 ASN cc_start: 0.8200 (t0) cc_final: 0.6951 (p0) REVERT: B 140 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7540 (mp) REVERT: B 149 PHE cc_start: 0.6284 (OUTLIER) cc_final: 0.5457 (m-80) REVERT: B 203 MET cc_start: 0.8137 (mmm) cc_final: 0.7765 (tpp) outliers start: 23 outliers final: 18 residues processed: 85 average time/residue: 0.1236 time to fit residues: 14.6814 Evaluate side-chains 88 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.218452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.191886 restraints weight = 7257.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.175834 restraints weight = 11559.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.175877 restraints weight = 9895.196| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5064 Z= 0.189 Angle : 0.725 12.836 6844 Z= 0.375 Chirality : 0.040 0.246 748 Planarity : 0.003 0.024 844 Dihedral : 5.194 56.814 643 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.29 % Allowed : 25.37 % Favored : 70.34 % 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: 2.54 (0.34), residues: 578 helix: 2.14 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -1.55 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.009 0.002 HIS A 53 PHE 0.033 0.001 PHE A 90 TYR 0.029 0.001 TYR B 234 ARG 0.004 0.000 ARG B 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1148.09 seconds wall clock time: 21 minutes 40.49 seconds (1300.49 seconds total)