Starting phenix.real_space_refine on Sun Mar 10 22:44:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdo_17616/03_2024/8pdo_17616.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdo_17616/03_2024/8pdo_17616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdo_17616/03_2024/8pdo_17616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdo_17616/03_2024/8pdo_17616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdo_17616/03_2024/8pdo_17616.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdo_17616/03_2024/8pdo_17616.pdb" } resolution = 3.1 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= -0.001 sd= 0.032 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 22 5.16 5 C 3564 2.51 5 N 990 2.21 5 O 1132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" 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: 5722 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "C" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'RNA': 14} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Time building chain proxies: 3.74, per 1000 atoms: 0.65 Number of scatterers: 5722 At special positions: 0 Unit cell: (114.45, 79.8, 82.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 14 15.00 O 1132 8.00 N 990 7.00 C 3564 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 69.1% alpha, 2.6% beta 0 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.595A pdb=" N TYR A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.620A pdb=" N LEU B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 120 through 141 Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.584A pdb=" N GLN B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 151 " --> pdb=" O GLN B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 156 through 171 removed outlier: 3.854A pdb=" N LYS B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.846A pdb=" N ARG B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.789A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 256 through 268 removed outlier: 3.613A pdb=" N ARG B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 296 removed outlier: 4.860A pdb=" N LYS B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.890A pdb=" N GLY B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 344 through 361 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG A 96 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 35 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 336 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 2.49 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: 1845 1.34 - 1.46: 846 1.46 - 1.57: 3079 1.57 - 1.69: 27 1.69 - 1.81: 38 Bond restraints: 5835 Sorted by residual: bond pdb=" C VAL A 35 " pdb=" N THR A 36 " ideal model delta sigma weight residual 1.331 1.303 0.027 1.24e-02 6.50e+03 4.88e+00 bond pdb=" CB VAL B 92 " pdb=" CG1 VAL B 92 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CA GLU B 20 " pdb=" C GLU B 20 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.66e-02 3.63e+03 3.98e+00 bond pdb=" CB VAL A 92 " pdb=" CG1 VAL A 92 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.63e+00 bond pdb=" N LYS B 239 " pdb=" CA LYS B 239 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.33e-02 5.65e+03 2.83e+00 ... (remaining 5830 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.47: 170 106.47 - 113.34: 3296 113.34 - 120.22: 2163 120.22 - 127.09: 2268 127.09 - 133.97: 41 Bond angle restraints: 7938 Sorted by residual: angle pdb=" C LEU A 52 " pdb=" N TYR A 53 " pdb=" CA TYR A 53 " ideal model delta sigma weight residual 122.60 115.45 7.15 1.56e+00 4.11e-01 2.10e+01 angle pdb=" N ILE A 6 " pdb=" CA ILE A 6 " pdb=" C ILE A 6 " ideal model delta sigma weight residual 106.21 108.97 -2.76 1.07e+00 8.73e-01 6.66e+00 angle pdb=" C GLN A 91 " pdb=" N VAL A 92 " pdb=" CA VAL A 92 " ideal model delta sigma weight residual 120.63 123.86 -3.23 1.33e+00 5.65e-01 5.91e+00 angle pdb=" N LYS B 239 " pdb=" CA LYS B 239 " pdb=" C LYS B 239 " ideal model delta sigma weight residual 112.54 109.71 2.83 1.22e+00 6.72e-01 5.38e+00 angle pdb=" CA GLU B 20 " pdb=" C GLU B 20 " pdb=" N SER B 21 " ideal model delta sigma weight residual 117.96 120.71 -2.75 1.23e+00 6.61e-01 4.98e+00 ... (remaining 7933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3187 17.53 - 35.05: 315 35.05 - 52.58: 59 52.58 - 70.11: 13 70.11 - 87.64: 21 Dihedral angle restraints: 3595 sinusoidal: 1563 harmonic: 2032 Sorted by residual: dihedral pdb=" CA GLY B 311 " pdb=" C GLY B 311 " pdb=" N LEU B 312 " pdb=" CA LEU B 312 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LEU B 52 " pdb=" C LEU B 52 " pdb=" N TYR B 53 " pdb=" CA TYR B 53 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ALA B 251 " pdb=" C ALA B 251 " pdb=" N TYR B 252 " pdb=" CA TYR B 252 " ideal model delta harmonic sigma weight residual -180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 652 0.042 - 0.083: 226 0.083 - 0.125: 48 0.125 - 0.166: 8 0.166 - 0.208: 2 Chirality restraints: 936 Sorted by residual: chirality pdb=" CB VAL B 35 " pdb=" CA VAL B 35 " pdb=" CG1 VAL B 35 " pdb=" CG2 VAL B 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA ILE A 25 " pdb=" N ILE A 25 " pdb=" C ILE A 25 " pdb=" CB ILE A 25 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 933 not shown) Planarity restraints: 962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 198 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A 199 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 53 " 0.007 2.00e-02 2.50e+03 1.34e-02 3.60e+00 pdb=" CG TYR A 53 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 53 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 53 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 53 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 53 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 53 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 53 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 73 " 0.025 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 C C 73 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C C 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C C 73 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C C 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C C 73 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C C 73 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C C 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 73 " -0.005 2.00e-02 2.50e+03 ... (remaining 959 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 51 2.63 - 3.20: 5295 3.20 - 3.77: 9054 3.77 - 4.33: 12859 4.33 - 4.90: 20585 Nonbonded interactions: 47844 Sorted by model distance: nonbonded pdb=" O LEU A 18 " pdb=" OG SER B 233 " model vdw 2.068 2.440 nonbonded pdb=" OG SER A 277 " pdb=" OD1 ASN A 320 " model vdw 2.138 2.440 nonbonded pdb=" O VAL A 35 " pdb=" OG1 THR A 95 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR A 338 " pdb=" OP2 C C 74 " model vdw 2.232 2.440 nonbonded pdb=" NH1 ARG A 27 " pdb=" O THR B 236 " model vdw 2.241 2.520 ... (remaining 47839 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 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: 2.610 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: 13.350 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.470 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.006 0.067 5835 Z= 0.418 Angle : 0.664 7.149 7938 Z= 0.393 Chirality : 0.044 0.208 936 Planarity : 0.004 0.051 962 Dihedral : 15.615 87.636 2291 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.19 (0.32), residues: 694 helix: 0.59 (0.24), residues: 470 sheet: -1.01 (0.87), residues: 30 loop : -0.60 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.004 0.001 HIS B 15 PHE 0.017 0.002 PHE B 224 TYR 0.031 0.003 TYR A 53 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.693 Fit side-chains REVERT: A 78 ARG cc_start: 0.7403 (mmm160) cc_final: 0.5880 (tpt-90) REVERT: A 249 MET cc_start: 0.7654 (mmt) cc_final: 0.7430 (mmt) REVERT: A 266 ARG cc_start: 0.7783 (tmt170) cc_final: 0.5836 (tpt170) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2626 time to fit residues: 27.2686 Evaluate side-chains 76 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 chunk 41 optimal weight: 0.4980 chunk 64 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5835 Z= 0.188 Angle : 0.468 6.115 7938 Z= 0.253 Chirality : 0.039 0.140 936 Planarity : 0.004 0.046 962 Dihedral : 11.402 73.943 987 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.34 % Allowed : 6.04 % Favored : 93.62 % 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: 0.91 (0.33), residues: 694 helix: 1.23 (0.24), residues: 474 sheet: -0.93 (0.89), residues: 30 loop : -0.59 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 275 PHE 0.012 0.001 PHE B 224 TYR 0.013 0.002 TYR A 53 ARG 0.006 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.641 Fit side-chains REVERT: A 78 ARG cc_start: 0.7439 (mmm160) cc_final: 0.5842 (tpt-90) REVERT: A 266 ARG cc_start: 0.7669 (tmt170) cc_final: 0.5078 (mtt180) outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.2896 time to fit residues: 26.6120 Evaluate side-chains 72 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5835 Z= 0.198 Angle : 0.453 6.073 7938 Z= 0.244 Chirality : 0.038 0.130 936 Planarity : 0.004 0.043 962 Dihedral : 11.338 73.918 987 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.17 % Allowed : 9.06 % Favored : 90.77 % 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: 1.16 (0.33), residues: 694 helix: 1.35 (0.25), residues: 476 sheet: -1.04 (0.88), residues: 30 loop : -0.25 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS B 15 PHE 0.011 0.001 PHE B 224 TYR 0.011 0.001 TYR A 59 ARG 0.005 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.642 Fit side-chains REVERT: A 78 ARG cc_start: 0.7445 (mmm160) cc_final: 0.5854 (tpt-90) REVERT: A 266 ARG cc_start: 0.7665 (tmt170) cc_final: 0.5041 (mtt180) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.2924 time to fit residues: 26.0975 Evaluate side-chains 68 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.0060 chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 0.0050 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5835 Z= 0.186 Angle : 0.441 5.957 7938 Z= 0.237 Chirality : 0.038 0.178 936 Planarity : 0.004 0.042 962 Dihedral : 11.307 73.932 987 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.67 % Allowed : 9.56 % Favored : 89.77 % 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: 1.31 (0.33), residues: 694 helix: 1.47 (0.25), residues: 476 sheet: -1.00 (0.88), residues: 30 loop : -0.21 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.010 0.001 PHE B 224 TYR 0.010 0.001 TYR A 59 ARG 0.008 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.662 Fit side-chains REVERT: A 78 ARG cc_start: 0.7412 (mmm160) cc_final: 0.5813 (tpt-90) REVERT: A 266 ARG cc_start: 0.7678 (tmt170) cc_final: 0.5084 (mtt180) REVERT: B 117 HIS cc_start: 0.7037 (t70) cc_final: 0.6589 (t70) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.2865 time to fit residues: 26.1987 Evaluate side-chains 71 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5835 Z= 0.268 Angle : 0.481 5.998 7938 Z= 0.257 Chirality : 0.040 0.170 936 Planarity : 0.004 0.039 962 Dihedral : 11.286 74.073 987 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.67 % Allowed : 11.24 % Favored : 88.09 % 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: 1.02 (0.33), residues: 694 helix: 1.27 (0.24), residues: 480 sheet: -1.06 (0.88), residues: 30 loop : -0.44 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.003 0.001 HIS B 15 PHE 0.012 0.002 PHE B 224 TYR 0.015 0.002 TYR A 59 ARG 0.007 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.711 Fit side-chains REVERT: A 78 ARG cc_start: 0.7446 (mmm160) cc_final: 0.5850 (tpt-90) REVERT: A 266 ARG cc_start: 0.7730 (tmt170) cc_final: 0.4988 (mtt180) REVERT: A 284 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7402 (tm-30) outliers start: 4 outliers final: 2 residues processed: 72 average time/residue: 0.2800 time to fit residues: 24.5273 Evaluate side-chains 71 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5835 Z= 0.196 Angle : 0.444 5.864 7938 Z= 0.238 Chirality : 0.038 0.142 936 Planarity : 0.004 0.039 962 Dihedral : 11.283 73.959 987 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.67 % Allowed : 12.42 % Favored : 86.91 % 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: 1.18 (0.33), residues: 694 helix: 1.43 (0.25), residues: 480 sheet: -1.13 (0.86), residues: 30 loop : -0.48 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.011 0.001 PHE B 224 TYR 0.011 0.001 TYR A 59 ARG 0.008 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.704 Fit side-chains REVERT: A 78 ARG cc_start: 0.7412 (mmm160) cc_final: 0.5816 (tpt-90) REVERT: A 266 ARG cc_start: 0.7696 (tmt170) cc_final: 0.4969 (mtt180) outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 0.2935 time to fit residues: 25.2887 Evaluate side-chains 71 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5835 Z= 0.173 Angle : 0.429 5.855 7938 Z= 0.231 Chirality : 0.038 0.125 936 Planarity : 0.004 0.039 962 Dihedral : 11.274 73.907 987 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.01 % Allowed : 12.75 % Favored : 86.24 % 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: 1.44 (0.33), residues: 694 helix: 1.61 (0.25), residues: 476 sheet: -1.18 (0.86), residues: 30 loop : -0.23 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.010 0.001 PHE B 224 TYR 0.010 0.001 TYR A 338 ARG 0.009 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.661 Fit side-chains REVERT: A 78 ARG cc_start: 0.7398 (mmm160) cc_final: 0.5801 (tpt-90) REVERT: A 266 ARG cc_start: 0.7653 (tmt170) cc_final: 0.4878 (mtt180) REVERT: A 284 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7446 (tm-30) REVERT: B 117 HIS cc_start: 0.7065 (t70) cc_final: 0.6630 (t70) outliers start: 6 outliers final: 4 residues processed: 75 average time/residue: 0.2668 time to fit residues: 24.4652 Evaluate side-chains 73 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5835 Z= 0.252 Angle : 0.469 5.877 7938 Z= 0.251 Chirality : 0.040 0.239 936 Planarity : 0.004 0.039 962 Dihedral : 11.264 74.066 987 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.01 % Allowed : 13.09 % Favored : 85.91 % 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: 1.17 (0.33), residues: 694 helix: 1.42 (0.24), residues: 480 sheet: -1.18 (0.87), residues: 30 loop : -0.45 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.002 0.001 HIS B 15 PHE 0.012 0.002 PHE B 224 TYR 0.014 0.002 TYR A 59 ARG 0.010 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.635 Fit side-chains REVERT: A 78 ARG cc_start: 0.7430 (mmm160) cc_final: 0.5831 (tpt-90) REVERT: A 266 ARG cc_start: 0.7682 (tmt170) cc_final: 0.5051 (mtt180) REVERT: A 284 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7437 (tm-30) outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.2749 time to fit residues: 23.7623 Evaluate side-chains 72 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 56 optimal weight: 0.7980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5835 Z= 0.174 Angle : 0.433 5.844 7938 Z= 0.232 Chirality : 0.038 0.184 936 Planarity : 0.004 0.039 962 Dihedral : 11.265 73.903 987 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.01 % Allowed : 13.09 % Favored : 85.91 % 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: 1.49 (0.33), residues: 694 helix: 1.67 (0.25), residues: 476 sheet: -1.56 (0.72), residues: 38 loop : -0.13 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.010 0.001 PHE B 224 TYR 0.010 0.001 TYR A 338 ARG 0.010 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.672 Fit side-chains REVERT: A 78 ARG cc_start: 0.7394 (mmm160) cc_final: 0.5802 (tpt-90) REVERT: A 266 ARG cc_start: 0.7615 (tmt170) cc_final: 0.5222 (mtp180) REVERT: A 284 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7353 (tm-30) REVERT: B 117 HIS cc_start: 0.7094 (t70) cc_final: 0.6579 (t70) outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 0.2689 time to fit residues: 24.5160 Evaluate side-chains 74 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5835 Z= 0.240 Angle : 0.467 5.848 7938 Z= 0.251 Chirality : 0.040 0.197 936 Planarity : 0.004 0.040 962 Dihedral : 11.259 74.100 987 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.01 % Allowed : 13.93 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.33), residues: 694 helix: 1.45 (0.24), residues: 482 sheet: -1.15 (0.88), residues: 30 loop : -0.38 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.002 0.001 HIS B 15 PHE 0.011 0.001 PHE B 224 TYR 0.014 0.002 TYR A 59 ARG 0.010 0.000 ARG B 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.710 Fit side-chains REVERT: A 78 ARG cc_start: 0.7423 (mmm160) cc_final: 0.5826 (tpt-90) REVERT: A 266 ARG cc_start: 0.7682 (tmt170) cc_final: 0.5273 (mtp180) REVERT: A 284 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 117 HIS cc_start: 0.7050 (t70) cc_final: 0.6616 (t70) outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.2740 time to fit residues: 24.1447 Evaluate side-chains 74 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.166024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144379 restraints weight = 6563.618| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.62 r_work: 0.3446 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5835 Z= 0.222 Angle : 0.461 5.866 7938 Z= 0.247 Chirality : 0.039 0.186 936 Planarity : 0.004 0.039 962 Dihedral : 11.256 74.057 987 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.84 % Allowed : 13.93 % Favored : 85.23 % 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: 1.26 (0.33), residues: 694 helix: 1.47 (0.24), residues: 482 sheet: -1.20 (0.87), residues: 30 loop : -0.37 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.011 0.001 PHE B 224 TYR 0.013 0.002 TYR A 59 ARG 0.010 0.000 ARG B 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.78 seconds wall clock time: 30 minutes 39.61 seconds (1839.61 seconds total)