Starting phenix.real_space_refine on Sun Mar 10 21:13:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/03_2024/8exr_28660_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/03_2024/8exr_28660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/03_2024/8exr_28660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/03_2024/8exr_28660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/03_2024/8exr_28660_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exr_28660/03_2024/8exr_28660_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 5 5.49 5 S 20 5.16 5 C 3438 2.51 5 N 802 2.21 5 O 844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 5111 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2496 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 6, 'TRANS': 288} Chain breaks: 1 Chain: "A" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 2051 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 6, 'TRANS': 234} Chain breaks: 1 Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.48, per 1000 atoms: 0.68 Number of scatterers: 5111 At special positions: 0 Unit cell: (72.38, 85.47, 93.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 20 16.00 P 5 15.00 O 844 8.00 N 802 7.00 C 3438 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: 2.00 Conformation dependent library (CDL) restraints added in 810.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 205 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 201 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 205 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 201 " 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 2 sheets defined 65.6% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'B' and resid 2 through 28 removed outlier: 3.771A pdb=" N TYR B 24 " --> pdb=" O PHE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 46 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 99 through 134 removed outlier: 3.990A pdb=" N THR B 107 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TRP B 110 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'B' and resid 184 through 188 removed outlier: 3.760A pdb=" N LYS B 188 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 208 removed outlier: 4.782A pdb=" N ILE B 199 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 223 removed outlier: 4.197A pdb=" N ILE B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 252 removed outlier: 4.462A pdb=" N ILE B 237 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 308 through 328 removed outlier: 3.922A pdb=" N PHE B 313 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 315 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 317 " --> pdb=" O ILE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'A' and resid 2 through 30 removed outlier: 3.529A pdb=" N ILE A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.625A pdb=" N LEU A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 45 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 133 removed outlier: 3.566A pdb=" N VAL A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 Processing helix chain 'A' and resid 195 through 208 removed outlier: 3.814A pdb=" N ASN A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 223 Processing helix chain 'A' and resid 228 through 252 removed outlier: 4.631A pdb=" N LYS A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG A 235 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 removed outlier: 4.741A pdb=" N LYS A 259 " --> pdb=" O ASN A 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 299 removed outlier: 3.734A pdb=" N LYS C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 328 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing sheet with id= A, first strand: chain 'B' and resid 160 through 164 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 164 296 hydrogen bonds defined for protein. 495 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: 1.14 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 1301 1.33 - 1.47: 1570 1.47 - 1.61: 2315 1.61 - 1.75: 3 1.75 - 1.89: 34 Bond restraints: 5223 Sorted by residual: bond pdb=" CB HIS B 213 " pdb=" CG HIS B 213 " ideal model delta sigma weight residual 1.497 1.371 0.126 1.40e-02 5.10e+03 8.05e+01 bond pdb=" CB HIS B 153 " pdb=" CG HIS B 153 " ideal model delta sigma weight residual 1.497 1.372 0.125 1.40e-02 5.10e+03 7.94e+01 bond pdb=" CB PHE A 173 " pdb=" CG PHE A 173 " ideal model delta sigma weight residual 1.502 1.321 0.181 2.30e-02 1.89e+03 6.18e+01 bond pdb=" NE1 TRP B 39 " pdb=" CE2 TRP B 39 " ideal model delta sigma weight residual 1.370 1.285 0.085 1.10e-02 8.26e+03 6.00e+01 bond pdb=" CB HIS A 205 " pdb=" CG HIS A 205 " ideal model delta sigma weight residual 1.497 1.389 0.108 1.40e-02 5.10e+03 5.93e+01 ... (remaining 5218 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.37: 151 106.37 - 113.27: 2656 113.27 - 120.16: 2302 120.16 - 127.06: 1867 127.06 - 133.96: 45 Bond angle restraints: 7021 Sorted by residual: angle pdb=" N VAL A 160 " pdb=" CA VAL A 160 " pdb=" C VAL A 160 " ideal model delta sigma weight residual 108.46 122.06 -13.60 1.49e+00 4.50e-01 8.33e+01 angle pdb=" N ARG A 194 " pdb=" CA ARG A 194 " pdb=" C ARG A 194 " ideal model delta sigma weight residual 114.04 102.97 11.07 1.24e+00 6.50e-01 7.97e+01 angle pdb=" N VAL B 160 " pdb=" CA VAL B 160 " pdb=" C VAL B 160 " ideal model delta sigma weight residual 108.46 121.66 -13.20 1.49e+00 4.50e-01 7.84e+01 angle pdb=" CA PHE B 30 " pdb=" CB PHE B 30 " pdb=" CG PHE B 30 " ideal model delta sigma weight residual 113.80 105.18 8.62 1.00e+00 1.00e+00 7.44e+01 angle pdb=" N TRP B 174 " pdb=" CA TRP B 174 " pdb=" C TRP B 174 " ideal model delta sigma weight residual 110.56 126.98 -16.42 1.94e+00 2.66e-01 7.16e+01 ... (remaining 7016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.09: 2907 14.09 - 28.17: 148 28.17 - 42.25: 49 42.25 - 56.34: 30 56.34 - 70.42: 11 Dihedral angle restraints: 3145 sinusoidal: 1362 harmonic: 1783 Sorted by residual: dihedral pdb=" C PHE B 258 " pdb=" N PHE B 258 " pdb=" CA PHE B 258 " pdb=" CB PHE B 258 " ideal model delta harmonic sigma weight residual -122.60 -114.82 -7.78 0 2.50e+00 1.60e-01 9.68e+00 dihedral pdb=" N TYR B 155 " pdb=" C TYR B 155 " pdb=" CA TYR B 155 " pdb=" CB TYR B 155 " ideal model delta harmonic sigma weight residual 122.80 130.57 -7.77 0 2.50e+00 1.60e-01 9.66e+00 dihedral pdb=" CG ARG A 235 " pdb=" CD ARG A 235 " pdb=" NE ARG A 235 " pdb=" CZ ARG A 235 " ideal model delta sinusoidal sigma weight residual 180.00 143.09 36.91 2 1.50e+01 4.44e-03 7.69e+00 ... (remaining 3142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 564 0.117 - 0.234: 200 0.234 - 0.351: 31 0.351 - 0.468: 4 0.468 - 0.584: 1 Chirality restraints: 800 Sorted by residual: chirality pdb=" C5 P6L A 702 " pdb=" C6 P6L A 702 " pdb=" C7 P6L A 702 " pdb=" O4 P6L A 702 " both_signs ideal model delta sigma weight residual False -2.31 -1.73 -0.58 2.00e-01 2.50e+01 8.54e+00 chirality pdb=" CA TRP B 174 " pdb=" N TRP B 174 " pdb=" C TRP B 174 " pdb=" CB TRP B 174 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA TYR B 155 " pdb=" N TYR B 155 " pdb=" C TYR B 155 " pdb=" CB TYR B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 797 not shown) Planarity restraints: 823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 P6L B 702 " 0.079 2.00e-02 2.50e+03 1.61e-01 2.59e+02 pdb=" C22 P6L B 702 " -0.213 2.00e-02 2.50e+03 pdb=" C23 P6L B 702 " 0.213 2.00e-02 2.50e+03 pdb=" C24 P6L B 702 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C21 P6L A 702 " 0.077 2.00e-02 2.50e+03 1.53e-01 2.35e+02 pdb=" C22 P6L A 702 " -0.203 2.00e-02 2.50e+03 pdb=" C23 P6L A 702 " 0.203 2.00e-02 2.50e+03 pdb=" C24 P6L A 702 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 P6L A 702 " -0.074 2.00e-02 2.50e+03 1.48e-01 2.18e+02 pdb=" C33 P6L A 702 " 0.195 2.00e-02 2.50e+03 pdb=" C34 P6L A 702 " -0.195 2.00e-02 2.50e+03 pdb=" C35 P6L A 702 " 0.074 2.00e-02 2.50e+03 ... (remaining 820 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 77 2.59 - 3.17: 5142 3.17 - 3.75: 7493 3.75 - 4.32: 10426 4.32 - 4.90: 15077 Nonbonded interactions: 38215 Sorted by model distance: nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.016 2.230 nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.017 2.230 nonbonded pdb=" OE1 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.038 2.230 nonbonded pdb=" OE1 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.050 2.230 nonbonded pdb=" O GLY B 286 " pdb=" CG LYS B 287 " model vdw 2.142 3.440 ... (remaining 38210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.120 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: 5.740 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.890 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.026 0.181 5223 Z= 1.635 Angle : 1.944 16.416 7021 Z= 1.328 Chirality : 0.115 0.584 800 Planarity : 0.013 0.161 823 Dihedral : 12.156 70.423 1981 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.76 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -0.66 (0.32), residues: 580 helix: -0.13 (0.24), residues: 383 sheet: -0.25 (0.87), residues: 26 loop : -0.87 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.009 TRP B 99 HIS 0.012 0.003 HIS A 153 PHE 0.033 0.006 PHE B 284 TYR 0.099 0.012 TYR A 203 ARG 0.006 0.001 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 41 LEU cc_start: 0.8542 (mt) cc_final: 0.7864 (tt) REVERT: B 136 LEU cc_start: 0.6840 (tp) cc_final: 0.6454 (tp) REVERT: B 255 LYS cc_start: 0.8736 (mttt) cc_final: 0.8205 (mmtm) REVERT: A 141 ASN cc_start: 0.7362 (m-40) cc_final: 0.6924 (p0) REVERT: A 187 PHE cc_start: 0.8156 (m-80) cc_final: 0.7907 (m-80) REVERT: A 219 ILE cc_start: 0.8605 (mm) cc_final: 0.8397 (mt) REVERT: A 276 ASN cc_start: 0.6779 (p0) cc_final: 0.6314 (m-40) REVERT: C 295 LEU cc_start: 0.8700 (mt) cc_final: 0.8423 (tt) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1908 time to fit residues: 44.0042 Evaluate side-chains 119 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5223 Z= 0.207 Angle : 0.664 7.434 7021 Z= 0.376 Chirality : 0.044 0.166 800 Planarity : 0.007 0.048 823 Dihedral : 13.307 70.820 725 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.24 % Favored : 97.41 % Rotamer: Outliers : 2.84 % Allowed : 11.88 % Favored : 85.28 % 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: -0.46 (0.32), residues: 580 helix: 0.07 (0.24), residues: 381 sheet: -0.04 (1.04), residues: 37 loop : -0.96 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 110 HIS 0.007 0.002 HIS B 213 PHE 0.020 0.002 PHE A 274 TYR 0.017 0.002 TYR B 226 ARG 0.007 0.001 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 MET cc_start: 0.7419 (mmt) cc_final: 0.6959 (mtp) REVERT: B 136 LEU cc_start: 0.6843 (tp) cc_final: 0.6317 (mp) REVERT: B 168 GLN cc_start: 0.6409 (mp10) cc_final: 0.6188 (mm-40) REVERT: A 122 LEU cc_start: 0.8160 (mt) cc_final: 0.7915 (tp) REVERT: C 295 LEU cc_start: 0.8326 (mt) cc_final: 0.7784 (tt) REVERT: C 300 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7803 (tm-30) outliers start: 16 outliers final: 10 residues processed: 154 average time/residue: 0.1583 time to fit residues: 31.5125 Evaluate side-chains 128 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain C residue 328 PHE 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: 0.8980 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.0030 chunk 52 optimal weight: 0.4980 chunk 57 optimal weight: 0.0270 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.4648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5223 Z= 0.172 Angle : 0.584 8.339 7021 Z= 0.323 Chirality : 0.042 0.242 800 Planarity : 0.006 0.051 823 Dihedral : 11.615 85.607 725 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.19 % Allowed : 15.43 % Favored : 81.38 % 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: -0.69 (0.33), residues: 580 helix: -0.07 (0.24), residues: 379 sheet: -0.06 (1.04), residues: 37 loop : -1.17 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 110 HIS 0.002 0.001 HIS A 201 PHE 0.013 0.002 PHE C 328 TYR 0.010 0.001 TYR B 175 ARG 0.007 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7438 (ttm-80) REVERT: B 136 LEU cc_start: 0.7175 (tp) cc_final: 0.6943 (mp) REVERT: B 203 TYR cc_start: 0.7058 (t80) cc_final: 0.6790 (t80) REVERT: A 7 MET cc_start: 0.6993 (mtt) cc_final: 0.6704 (mtm) REVERT: A 22 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7671 (t80) REVERT: A 122 LEU cc_start: 0.8245 (mt) cc_final: 0.8033 (tp) REVERT: C 287 LYS cc_start: 0.7511 (ttmt) cc_final: 0.7175 (mttp) REVERT: C 295 LEU cc_start: 0.8336 (mt) cc_final: 0.7781 (tt) outliers start: 18 outliers final: 12 residues processed: 142 average time/residue: 0.1572 time to fit residues: 29.1601 Evaluate side-chains 129 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 0.3980 chunk 25 optimal weight: 0.0570 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 0.0040 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS A 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5223 Z= 0.151 Angle : 0.548 7.836 7021 Z= 0.303 Chirality : 0.040 0.188 800 Planarity : 0.006 0.047 823 Dihedral : 10.420 73.227 725 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.84 % Allowed : 16.84 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.33), residues: 580 helix: 0.03 (0.25), residues: 373 sheet: -0.44 (1.02), residues: 37 loop : -1.09 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.002 0.000 HIS B 213 PHE 0.013 0.001 PHE C 317 TYR 0.026 0.001 TYR A 175 ARG 0.004 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: B 23 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7572 (tpp80) REVERT: B 203 TYR cc_start: 0.7122 (t80) cc_final: 0.6710 (t80) REVERT: A 165 GLU cc_start: 0.6675 (pm20) cc_final: 0.6374 (pt0) outliers start: 16 outliers final: 9 residues processed: 134 average time/residue: 0.1582 time to fit residues: 27.6584 Evaluate side-chains 121 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5223 Z= 0.223 Angle : 0.631 8.466 7021 Z= 0.348 Chirality : 0.042 0.183 800 Planarity : 0.006 0.046 823 Dihedral : 10.766 80.928 725 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.72 % Allowed : 18.26 % Favored : 78.01 % 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: -1.00 (0.33), residues: 580 helix: -0.13 (0.25), residues: 373 sheet: -0.81 (0.94), residues: 37 loop : -1.57 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 39 HIS 0.005 0.001 HIS B 213 PHE 0.017 0.002 PHE A 173 TYR 0.021 0.002 TYR B 155 ARG 0.005 0.001 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: C 295 LEU cc_start: 0.8363 (mt) cc_final: 0.7684 (tt) outliers start: 21 outliers final: 18 residues processed: 134 average time/residue: 0.1407 time to fit residues: 25.0642 Evaluate side-chains 134 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 309 LEU 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: 0.9980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN A 152 ASN A 278 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5223 Z= 0.157 Angle : 0.538 6.646 7021 Z= 0.302 Chirality : 0.039 0.167 800 Planarity : 0.006 0.046 823 Dihedral : 10.197 73.175 725 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.19 % Allowed : 20.57 % Favored : 76.24 % 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: -0.70 (0.34), residues: 580 helix: 0.07 (0.27), residues: 365 sheet: -0.62 (0.96), residues: 37 loop : -1.33 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 174 HIS 0.005 0.001 HIS B 213 PHE 0.025 0.001 PHE B 151 TYR 0.009 0.001 TYR B 175 ARG 0.003 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6627 (tpp) cc_final: 0.6418 (tpp) REVERT: B 100 ASP cc_start: 0.7304 (t0) cc_final: 0.6971 (m-30) REVERT: A 123 LYS cc_start: 0.8018 (pttm) cc_final: 0.7329 (pttm) REVERT: A 165 GLU cc_start: 0.7158 (pm20) cc_final: 0.6716 (pt0) REVERT: A 246 ASP cc_start: 0.6583 (t0) cc_final: 0.6252 (t0) outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 0.1532 time to fit residues: 26.3659 Evaluate side-chains 128 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5223 Z= 0.154 Angle : 0.542 7.270 7021 Z= 0.298 Chirality : 0.039 0.187 800 Planarity : 0.005 0.033 823 Dihedral : 9.906 74.980 725 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.01 % Allowed : 20.92 % Favored : 76.06 % 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: -0.70 (0.34), residues: 580 helix: 0.07 (0.26), residues: 367 sheet: -0.49 (0.97), residues: 37 loop : -1.38 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.005 0.001 HIS B 213 PHE 0.027 0.001 PHE C 328 TYR 0.045 0.001 TYR B 175 ARG 0.003 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7344 (t0) cc_final: 0.7006 (m-30) REVERT: A 123 LYS cc_start: 0.8049 (pttm) cc_final: 0.7406 (ptpt) REVERT: A 165 GLU cc_start: 0.7246 (pm20) cc_final: 0.6749 (pt0) REVERT: A 187 PHE cc_start: 0.7883 (m-80) cc_final: 0.7676 (m-80) REVERT: A 246 ASP cc_start: 0.6605 (t0) cc_final: 0.6268 (t0) REVERT: C 295 LEU cc_start: 0.8279 (mt) cc_final: 0.7669 (tt) outliers start: 17 outliers final: 13 residues processed: 134 average time/residue: 0.1570 time to fit residues: 27.6968 Evaluate side-chains 131 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5223 Z= 0.176 Angle : 0.552 7.039 7021 Z= 0.308 Chirality : 0.040 0.172 800 Planarity : 0.005 0.050 823 Dihedral : 10.058 82.392 725 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.72 % Allowed : 21.99 % Favored : 74.29 % 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: -0.64 (0.34), residues: 580 helix: 0.10 (0.27), residues: 358 sheet: -0.86 (0.95), residues: 36 loop : -1.16 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 174 HIS 0.006 0.001 HIS B 213 PHE 0.023 0.001 PHE C 328 TYR 0.019 0.002 TYR B 175 ARG 0.002 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 211 THR cc_start: 0.7909 (p) cc_final: 0.7597 (p) REVERT: B 285 ASN cc_start: 0.6494 (m110) cc_final: 0.5999 (m-40) REVERT: A 246 ASP cc_start: 0.6865 (t0) cc_final: 0.6544 (t0) outliers start: 21 outliers final: 16 residues processed: 137 average time/residue: 0.1402 time to fit residues: 25.5386 Evaluate side-chains 131 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.6741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5223 Z= 0.158 Angle : 0.558 7.203 7021 Z= 0.307 Chirality : 0.040 0.172 800 Planarity : 0.005 0.054 823 Dihedral : 9.944 86.733 725 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.84 % Allowed : 24.29 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.34), residues: 580 helix: 0.12 (0.27), residues: 359 sheet: -0.88 (0.97), residues: 36 loop : -1.14 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.003 0.001 HIS A 213 PHE 0.023 0.001 PHE C 328 TYR 0.036 0.002 TYR A 175 ARG 0.003 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 203 TYR cc_start: 0.7219 (t80) cc_final: 0.6808 (t80) REVERT: B 285 ASN cc_start: 0.6393 (m110) cc_final: 0.6096 (m-40) REVERT: A 246 ASP cc_start: 0.6752 (t0) cc_final: 0.6453 (t0) REVERT: C 295 LEU cc_start: 0.8243 (mt) cc_final: 0.7653 (tt) outliers start: 16 outliers final: 12 residues processed: 128 average time/residue: 0.1456 time to fit residues: 24.8559 Evaluate side-chains 125 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.0170 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.0470 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 0.0010 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5223 Z= 0.148 Angle : 0.572 10.868 7021 Z= 0.307 Chirality : 0.040 0.166 800 Planarity : 0.005 0.050 823 Dihedral : 9.595 89.849 725 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.60 % Allowed : 25.71 % Favored : 72.70 % 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: -0.60 (0.35), residues: 580 helix: 0.10 (0.27), residues: 359 sheet: -0.78 (1.00), residues: 36 loop : -1.09 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 174 HIS 0.002 0.000 HIS A 213 PHE 0.022 0.001 PHE C 328 TYR 0.037 0.002 TYR B 175 ARG 0.003 0.000 ARG B 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 203 TYR cc_start: 0.7178 (t80) cc_final: 0.6740 (t80) REVERT: A 246 ASP cc_start: 0.6490 (t0) cc_final: 0.6165 (t0) REVERT: C 330 MET cc_start: 0.4256 (tmm) cc_final: 0.3300 (tpt) outliers start: 9 outliers final: 6 residues processed: 130 average time/residue: 0.1421 time to fit residues: 24.6749 Evaluate side-chains 127 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 275 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.183736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161625 restraints weight = 10632.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.166000 restraints weight = 6388.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.168998 restraints weight = 4369.173| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.7067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5223 Z= 0.169 Angle : 0.605 10.751 7021 Z= 0.318 Chirality : 0.040 0.167 800 Planarity : 0.005 0.049 823 Dihedral : 9.702 87.218 725 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.48 % Allowed : 26.06 % Favored : 71.45 % 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: -0.69 (0.34), residues: 580 helix: 0.09 (0.27), residues: 358 sheet: -0.91 (0.98), residues: 36 loop : -1.23 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 174 HIS 0.004 0.001 HIS B 213 PHE 0.021 0.001 PHE C 328 TYR 0.029 0.002 TYR A 175 ARG 0.002 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1468.06 seconds wall clock time: 27 minutes 16.04 seconds (1636.04 seconds total)