Starting phenix.real_space_refine on Fri Nov 15 00:25:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/11_2024/8izf_35863.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/11_2024/8izf_35863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/11_2024/8izf_35863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/11_2024/8izf_35863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/11_2024/8izf_35863.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/11_2024/8izf_35863.cif" } resolution = 3.85 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= 0.004 sd= 0.052 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 2 5.49 5 S 38 5.16 5 C 5088 2.51 5 N 1202 2.21 5 O 1264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7594 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2670 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1087 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Restraints were copied for chains: C, D Time building chain proxies: 5.69, per 1000 atoms: 0.75 Number of scatterers: 7594 At special positions: 0 Unit cell: (110.416, 101.84, 100.768, 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 38 16.00 P 2 15.00 O 1264 8.00 N 1202 7.00 C 5088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.1 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 67.0% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.530A pdb=" N PHE A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 100 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 130 through 162 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 167 through 196 Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 217 through 241 Processing helix chain 'A' and resid 249 through 269 Processing helix chain 'A' and resid 275 through 298 removed outlier: 3.786A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 335 removed outlier: 3.947A pdb=" N TYR A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 384 removed outlier: 3.881A pdb=" N ILE A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 47 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.736A pdb=" N HIS B 52 " --> pdb=" O TYR B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 52' Processing helix chain 'B' and resid 76 through 92 removed outlier: 3.541A pdb=" N TYR B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.523A pdb=" N VAL B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 84 through 100 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 130 through 162 Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 167 through 196 Proline residue: C 188 - end of helix Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 217 through 241 Processing helix chain 'C' and resid 249 through 269 Processing helix chain 'C' and resid 275 through 298 removed outlier: 3.786A pdb=" N LEU C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 335 removed outlier: 3.946A pdb=" N TYR C 320 " --> pdb=" O TYR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 384 removed outlier: 3.881A pdb=" N ILE C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 47 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.736A pdb=" N HIS D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 52' Processing helix chain 'D' and resid 76 through 92 removed outlier: 3.541A pdb=" N TYR D 92 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 142 removed outlier: 3.524A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 53 through 59 removed outlier: 3.616A pdb=" N VAL B 129 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 59 removed outlier: 3.616A pdb=" N VAL D 129 " --> pdb=" O ILE D 65 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1434 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: 2.15 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1096 1.32 - 1.44: 2532 1.44 - 1.57: 4158 1.57 - 1.70: 2 1.70 - 1.83: 58 Bond restraints: 7846 Sorted by residual: bond pdb=" C31 6PL D 201 " pdb=" O2 6PL D 201 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C31 6PL B 201 " pdb=" O2 6PL B 201 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C11 6PL D 201 " pdb=" O3 6PL D 201 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C11 6PL B 201 " pdb=" O3 6PL B 201 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" CA PHE A 343 " pdb=" CB PHE A 343 " ideal model delta sigma weight residual 1.530 1.462 0.068 1.69e-02 3.50e+03 1.62e+01 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 10531 3.86 - 7.73: 101 7.73 - 11.59: 8 11.59 - 15.46: 8 15.46 - 19.32: 4 Bond angle restraints: 10652 Sorted by residual: angle pdb=" N PHE C 343 " pdb=" CA PHE C 343 " pdb=" C PHE C 343 " ideal model delta sigma weight residual 110.80 130.12 -19.32 2.13e+00 2.20e-01 8.23e+01 angle pdb=" N PHE A 343 " pdb=" CA PHE A 343 " pdb=" C PHE A 343 " ideal model delta sigma weight residual 110.80 130.08 -19.28 2.13e+00 2.20e-01 8.20e+01 angle pdb=" N LYS C 247 " pdb=" CA LYS C 247 " pdb=" C LYS C 247 " ideal model delta sigma weight residual 110.24 98.33 11.91 1.41e+00 5.03e-01 7.13e+01 angle pdb=" N LYS A 247 " pdb=" CA LYS A 247 " pdb=" C LYS A 247 " ideal model delta sigma weight residual 110.24 98.35 11.89 1.41e+00 5.03e-01 7.11e+01 angle pdb=" N MET A 140 " pdb=" CA MET A 140 " pdb=" C MET A 140 " ideal model delta sigma weight residual 111.36 103.42 7.94 1.09e+00 8.42e-01 5.31e+01 ... (remaining 10647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 3953 18.05 - 36.09: 410 36.09 - 54.14: 98 54.14 - 72.19: 16 72.19 - 90.24: 15 Dihedral angle restraints: 4492 sinusoidal: 1828 harmonic: 2664 Sorted by residual: dihedral pdb=" CA GLU D 118 " pdb=" C GLU D 118 " pdb=" N ASP D 119 " pdb=" CA ASP D 119 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLU B 118 " pdb=" C GLU B 118 " pdb=" N ASP B 119 " pdb=" CA ASP B 119 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA CYS B 53 " pdb=" CB CYS B 53 " pdb=" SG CYS B 53 " pdb=" SG CYS B 75 " ideal model delta sinusoidal sigma weight residual -73.00 2.17 -75.17 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 4489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1107 0.118 - 0.236: 27 0.236 - 0.354: 2 0.354 - 0.472: 0 0.472 - 0.590: 2 Chirality restraints: 1138 Sorted by residual: chirality pdb=" CA PHE C 343 " pdb=" N PHE C 343 " pdb=" C PHE C 343 " pdb=" CB PHE C 343 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" CA PHE A 343 " pdb=" N PHE A 343 " pdb=" C PHE A 343 " pdb=" CB PHE A 343 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CA LYS C 247 " pdb=" N LYS C 247 " pdb=" C LYS C 247 " pdb=" CB LYS C 247 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1135 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 139 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" C TYR A 139 " 0.067 2.00e-02 2.50e+03 pdb=" O TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" N MET A 140 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 139 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C TYR C 139 " -0.067 2.00e-02 2.50e+03 pdb=" O TYR C 139 " 0.026 2.00e-02 2.50e+03 pdb=" N MET C 140 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 77 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS D 77 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS D 77 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG D 78 " -0.019 2.00e-02 2.50e+03 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 67 2.54 - 3.13: 6465 3.13 - 3.72: 12007 3.72 - 4.31: 15506 4.31 - 4.90: 25341 Nonbonded interactions: 59386 Sorted by model distance: nonbonded pdb=" O ILE B 103 " pdb=" OH TYR D 148 " model vdw 1.945 3.040 nonbonded pdb=" OH TYR B 148 " pdb=" O ILE D 103 " model vdw 1.952 3.040 nonbonded pdb=" O LYS A 244 " pdb=" O PRO A 245 " model vdw 2.010 3.040 nonbonded pdb=" O LYS C 244 " pdb=" O PRO C 245 " model vdw 2.011 3.040 nonbonded pdb=" SG CYS D 102 " pdb=" SG CYS D 142 " model vdw 2.029 3.760 ... (remaining 59381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.630 Find NCS groups from input model: 0.210 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 0.100 7846 Z= 0.386 Angle : 1.095 19.322 10652 Z= 0.624 Chirality : 0.057 0.590 1138 Planarity : 0.006 0.063 1296 Dihedral : 16.149 90.235 2778 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.48 % Favored : 89.84 % Rotamer: Outliers : 2.73 % Allowed : 1.74 % Favored : 95.53 % 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: -1.59 (0.27), residues: 886 helix: 0.25 (0.20), residues: 562 sheet: -1.68 (0.58), residues: 58 loop : -3.81 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 50 HIS 0.008 0.001 HIS A 249 PHE 0.020 0.002 PHE A 271 TYR 0.032 0.002 TYR C 279 ARG 0.011 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 294 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 TRP cc_start: 0.8276 (p-90) cc_final: 0.7844 (p-90) REVERT: A 168 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6197 (m90) REVERT: A 174 MET cc_start: 0.8632 (mmt) cc_final: 0.8164 (mmt) REVERT: A 182 TYR cc_start: 0.7918 (p90) cc_final: 0.7554 (t80) REVERT: A 236 CYS cc_start: 0.8676 (p) cc_final: 0.8464 (p) REVERT: A 251 GLU cc_start: 0.7857 (pm20) cc_final: 0.7460 (pm20) REVERT: A 289 LEU cc_start: 0.8881 (tp) cc_final: 0.8583 (tt) REVERT: A 334 ARG cc_start: 0.7006 (tmt170) cc_final: 0.6782 (tpt170) REVERT: A 343 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7782 (t80) REVERT: A 346 GLN cc_start: 0.8589 (mp10) cc_final: 0.8219 (mp10) REVERT: C 84 TRP cc_start: 0.8268 (p-90) cc_final: 0.7829 (p-90) REVERT: C 168 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6175 (m90) REVERT: C 174 MET cc_start: 0.8753 (mmt) cc_final: 0.8269 (mmt) REVERT: C 236 CYS cc_start: 0.8675 (p) cc_final: 0.8460 (p) REVERT: C 251 GLU cc_start: 0.7866 (pm20) cc_final: 0.7509 (pm20) REVERT: C 334 ARG cc_start: 0.6939 (tmt170) cc_final: 0.6230 (ttt180) REVERT: C 343 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7799 (t80) REVERT: C 346 GLN cc_start: 0.8577 (mp10) cc_final: 0.8175 (mp10) REVERT: D 65 ILE cc_start: 0.9318 (pt) cc_final: 0.9083 (pt) outliers start: 22 outliers final: 4 residues processed: 306 average time/residue: 0.1821 time to fit residues: 76.3728 Evaluate side-chains 212 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 332 GLN ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS C 332 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7846 Z= 0.216 Angle : 0.723 13.481 10652 Z= 0.372 Chirality : 0.043 0.143 1138 Planarity : 0.005 0.056 1296 Dihedral : 9.672 54.880 1084 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 4.22 % Allowed : 16.63 % Favored : 79.16 % 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: -0.87 (0.28), residues: 886 helix: 0.91 (0.21), residues: 546 sheet: -1.67 (0.58), residues: 58 loop : -3.44 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 68 HIS 0.005 0.001 HIS A 82 PHE 0.031 0.002 PHE A 158 TYR 0.031 0.002 TYR C 182 ARG 0.003 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 TRP cc_start: 0.8103 (p-90) cc_final: 0.7802 (p-90) REVERT: A 140 MET cc_start: 0.8405 (tpp) cc_final: 0.7819 (tpp) REVERT: A 168 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6600 (m90) REVERT: A 332 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: A 334 ARG cc_start: 0.6122 (tmt170) cc_final: 0.5472 (ttt180) REVERT: A 343 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7903 (t80) REVERT: A 357 VAL cc_start: 0.7687 (t) cc_final: 0.7469 (p) REVERT: B 28 PHE cc_start: 0.8706 (t80) cc_final: 0.8496 (t80) REVERT: B 148 TYR cc_start: 0.7754 (m-80) cc_final: 0.7459 (m-80) REVERT: C 84 TRP cc_start: 0.8097 (p-90) cc_final: 0.7804 (p-90) REVERT: C 168 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6579 (m90) REVERT: C 332 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: C 334 ARG cc_start: 0.6124 (tmt170) cc_final: 0.5490 (ttt180) REVERT: C 343 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7943 (t80) REVERT: C 370 TYR cc_start: 0.7899 (t80) cc_final: 0.7649 (t80) REVERT: D 65 ILE cc_start: 0.9193 (pt) cc_final: 0.8943 (pt) REVERT: D 148 TYR cc_start: 0.7797 (m-80) cc_final: 0.7504 (m-80) REVERT: D 150 MET cc_start: 0.7345 (ttp) cc_final: 0.6787 (ptm) outliers start: 34 outliers final: 23 residues processed: 268 average time/residue: 0.1676 time to fit residues: 63.3528 Evaluate side-chains 238 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 339 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.0070 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 332 GLN B 52 HIS C 82 HIS C 332 GLN D 52 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7846 Z= 0.203 Angle : 0.682 9.340 10652 Z= 0.354 Chirality : 0.043 0.231 1138 Planarity : 0.005 0.052 1296 Dihedral : 8.957 57.845 1082 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.84 % Allowed : 20.10 % Favored : 75.06 % 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: -0.71 (0.28), residues: 886 helix: 0.99 (0.21), residues: 546 sheet: -0.76 (0.62), residues: 54 loop : -3.46 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 72 HIS 0.009 0.001 HIS C 82 PHE 0.027 0.001 PHE A 158 TYR 0.023 0.002 TYR C 279 ARG 0.003 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 1.030 Fit side-chains REVERT: A 168 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6767 (m90) REVERT: A 224 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7070 (t80) REVERT: A 248 ASP cc_start: 0.7335 (t70) cc_final: 0.6599 (t0) REVERT: A 334 ARG cc_start: 0.6208 (tmt170) cc_final: 0.5516 (ttt180) REVERT: A 343 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7905 (t80) REVERT: B 28 PHE cc_start: 0.8679 (t80) cc_final: 0.8380 (t80) REVERT: B 38 GLU cc_start: 0.8019 (tp30) cc_final: 0.7818 (tp30) REVERT: B 148 TYR cc_start: 0.7912 (m-80) cc_final: 0.7616 (m-80) REVERT: C 168 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.6761 (m90) REVERT: C 224 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7070 (t80) REVERT: C 334 ARG cc_start: 0.6152 (tmt170) cc_final: 0.5512 (ttt180) REVERT: C 343 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7894 (t80) REVERT: D 28 PHE cc_start: 0.8450 (t80) cc_final: 0.8241 (t80) REVERT: D 92 TYR cc_start: 0.8311 (m-10) cc_final: 0.7967 (m-10) REVERT: D 148 TYR cc_start: 0.7913 (m-80) cc_final: 0.7645 (m-80) outliers start: 39 outliers final: 18 residues processed: 262 average time/residue: 0.1620 time to fit residues: 59.3095 Evaluate side-chains 233 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7846 Z= 0.273 Angle : 0.709 10.514 10652 Z= 0.366 Chirality : 0.044 0.206 1138 Planarity : 0.005 0.050 1296 Dihedral : 8.590 59.861 1082 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 6.33 % Allowed : 23.08 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.28), residues: 886 helix: 0.94 (0.21), residues: 552 sheet: -0.93 (0.61), residues: 56 loop : -3.71 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 72 HIS 0.007 0.001 HIS A 319 PHE 0.030 0.002 PHE C 158 TYR 0.024 0.002 TYR A 182 ARG 0.004 0.001 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 220 time to evaluate : 1.000 Fit side-chains REVERT: A 168 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.6824 (m90) REVERT: A 224 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7062 (t80) REVERT: A 233 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: A 248 ASP cc_start: 0.7383 (t70) cc_final: 0.6708 (t0) REVERT: A 251 GLU cc_start: 0.7694 (pm20) cc_final: 0.7404 (pm20) REVERT: A 334 ARG cc_start: 0.6313 (tmt170) cc_final: 0.5562 (ttt180) REVERT: A 343 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7815 (t80) REVERT: A 369 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8772 (mm) REVERT: B 28 PHE cc_start: 0.8681 (t80) cc_final: 0.8416 (t80) REVERT: B 149 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6894 (p90) REVERT: C 140 MET cc_start: 0.8507 (tpp) cc_final: 0.8291 (mtt) REVERT: C 168 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.6817 (m90) REVERT: C 224 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7075 (t80) REVERT: C 248 ASP cc_start: 0.7488 (t0) cc_final: 0.6699 (t0) REVERT: C 251 GLU cc_start: 0.7787 (pm20) cc_final: 0.7571 (pm20) REVERT: C 334 ARG cc_start: 0.6274 (tmt170) cc_final: 0.5519 (ttt180) REVERT: C 343 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7877 (t80) REVERT: D 28 PHE cc_start: 0.8469 (t80) cc_final: 0.8268 (t80) REVERT: D 38 GLU cc_start: 0.8087 (tp30) cc_final: 0.7872 (tp30) REVERT: D 149 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.6884 (p90) outliers start: 51 outliers final: 34 residues processed: 248 average time/residue: 0.1631 time to fit residues: 57.6076 Evaluate side-chains 249 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 149 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7796 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7846 Z= 0.210 Angle : 0.680 9.685 10652 Z= 0.351 Chirality : 0.042 0.178 1138 Planarity : 0.005 0.050 1296 Dihedral : 8.203 59.407 1082 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 5.96 % Allowed : 25.19 % Favored : 68.86 % 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: -0.74 (0.28), residues: 886 helix: 1.03 (0.21), residues: 552 sheet: -0.69 (0.65), residues: 56 loop : -3.73 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 68 HIS 0.004 0.001 HIS A 319 PHE 0.030 0.002 PHE C 158 TYR 0.019 0.001 TYR B 42 ARG 0.004 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.932 Fit side-chains REVERT: A 168 HIS cc_start: 0.7364 (m170) cc_final: 0.6918 (m90) REVERT: A 224 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.6947 (t80) REVERT: A 233 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: A 248 ASP cc_start: 0.7298 (t70) cc_final: 0.6618 (t0) REVERT: A 251 GLU cc_start: 0.7422 (pm20) cc_final: 0.6988 (pm20) REVERT: A 323 LEU cc_start: 0.8612 (mm) cc_final: 0.8392 (tp) REVERT: A 334 ARG cc_start: 0.6322 (tmt170) cc_final: 0.5526 (ttt180) REVERT: A 343 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7864 (t80) REVERT: B 28 PHE cc_start: 0.8688 (t80) cc_final: 0.8436 (t80) REVERT: B 149 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6867 (p90) REVERT: C 168 HIS cc_start: 0.7411 (m170) cc_final: 0.6969 (m90) REVERT: C 224 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7015 (t80) REVERT: C 248 ASP cc_start: 0.7401 (t0) cc_final: 0.6686 (t0) REVERT: C 251 GLU cc_start: 0.7586 (pm20) cc_final: 0.7287 (pm20) REVERT: C 334 ARG cc_start: 0.6230 (tmt170) cc_final: 0.5494 (ttt180) REVERT: C 343 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7895 (t80) REVERT: D 28 PHE cc_start: 0.8483 (t80) cc_final: 0.8213 (t80) REVERT: D 100 SER cc_start: 0.8345 (OUTLIER) cc_final: 0.8093 (m) REVERT: D 149 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6851 (p90) outliers start: 48 outliers final: 29 residues processed: 259 average time/residue: 0.1538 time to fit residues: 57.1655 Evaluate side-chains 259 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 149 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7846 Z= 0.236 Angle : 0.712 10.111 10652 Z= 0.364 Chirality : 0.043 0.160 1138 Planarity : 0.005 0.049 1296 Dihedral : 7.817 59.948 1078 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 5.58 % Allowed : 27.30 % Favored : 67.12 % 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: -0.73 (0.28), residues: 886 helix: 0.95 (0.21), residues: 554 sheet: -0.38 (0.65), residues: 56 loop : -3.64 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 84 HIS 0.004 0.001 HIS D 52 PHE 0.038 0.002 PHE C 158 TYR 0.026 0.002 TYR C 182 ARG 0.004 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 0.818 Fit side-chains REVERT: A 168 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.7025 (m90) REVERT: A 224 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.6928 (t80) REVERT: A 323 LEU cc_start: 0.8636 (mm) cc_final: 0.8430 (tp) REVERT: A 334 ARG cc_start: 0.6318 (tmt170) cc_final: 0.5515 (ttt180) REVERT: B 28 PHE cc_start: 0.8687 (t80) cc_final: 0.8468 (t80) REVERT: B 149 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6859 (p90) REVERT: C 224 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.6978 (t80) REVERT: C 248 ASP cc_start: 0.7443 (t0) cc_final: 0.6779 (t0) REVERT: C 251 GLU cc_start: 0.7525 (pm20) cc_final: 0.7159 (pm20) REVERT: C 334 ARG cc_start: 0.6311 (tmt170) cc_final: 0.5502 (ttt180) REVERT: D 28 PHE cc_start: 0.8524 (t80) cc_final: 0.8296 (t80) REVERT: D 93 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6661 (tm-30) REVERT: D 149 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.6764 (p90) outliers start: 45 outliers final: 33 residues processed: 250 average time/residue: 0.1606 time to fit residues: 57.2642 Evaluate side-chains 255 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 149 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 8.9990 chunk 48 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 0.0050 chunk 84 optimal weight: 0.0070 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7846 Z= 0.194 Angle : 0.707 9.517 10652 Z= 0.363 Chirality : 0.042 0.152 1138 Planarity : 0.005 0.049 1296 Dihedral : 7.247 58.257 1074 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.85 % Allowed : 28.66 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.28), residues: 886 helix: 1.09 (0.21), residues: 550 sheet: -0.38 (0.65), residues: 56 loop : -3.55 (0.31), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 84 HIS 0.003 0.001 HIS D 52 PHE 0.029 0.002 PHE C 373 TYR 0.020 0.001 TYR D 42 ARG 0.003 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.833 Fit side-chains REVERT: A 233 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: A 334 ARG cc_start: 0.6145 (tmt170) cc_final: 0.5398 (ttt180) REVERT: B 28 PHE cc_start: 0.8713 (t80) cc_final: 0.8427 (t80) REVERT: B 149 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6698 (p90) REVERT: C 91 LEU cc_start: 0.8024 (pp) cc_final: 0.7804 (pp) REVERT: C 140 MET cc_start: 0.8475 (tpp) cc_final: 0.8180 (tpp) REVERT: C 224 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7057 (t80) REVERT: C 334 ARG cc_start: 0.6132 (tmt170) cc_final: 0.5464 (ttt180) REVERT: D 28 PHE cc_start: 0.8529 (t80) cc_final: 0.8278 (t80) outliers start: 31 outliers final: 23 residues processed: 257 average time/residue: 0.1672 time to fit residues: 59.6636 Evaluate side-chains 254 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7846 Z= 0.212 Angle : 0.719 9.812 10652 Z= 0.368 Chirality : 0.043 0.152 1138 Planarity : 0.005 0.048 1296 Dihedral : 7.049 57.625 1072 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.84 % Allowed : 26.92 % Favored : 68.24 % 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: -0.53 (0.28), residues: 886 helix: 1.07 (0.21), residues: 554 sheet: -0.37 (0.66), residues: 56 loop : -3.46 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 68 HIS 0.004 0.001 HIS B 52 PHE 0.027 0.002 PHE C 373 TYR 0.026 0.001 TYR B 92 ARG 0.003 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8174 (pp) cc_final: 0.7949 (pp) REVERT: A 140 MET cc_start: 0.8584 (tpp) cc_final: 0.7881 (tpp) REVERT: A 233 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: A 334 ARG cc_start: 0.6169 (tmt170) cc_final: 0.5354 (ttm170) REVERT: B 28 PHE cc_start: 0.8719 (t80) cc_final: 0.8442 (t80) REVERT: B 149 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.6319 (p90) REVERT: C 91 LEU cc_start: 0.8185 (pp) cc_final: 0.7965 (pp) REVERT: C 140 MET cc_start: 0.8524 (tpp) cc_final: 0.8288 (mtt) REVERT: C 224 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7335 (t80) REVERT: C 334 ARG cc_start: 0.6204 (tmt170) cc_final: 0.5411 (ttt180) REVERT: C 342 ASN cc_start: 0.7355 (t0) cc_final: 0.7118 (t0) REVERT: D 28 PHE cc_start: 0.8532 (t80) cc_final: 0.8294 (t80) REVERT: D 149 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.6505 (p90) outliers start: 39 outliers final: 32 residues processed: 253 average time/residue: 0.1688 time to fit residues: 59.7543 Evaluate side-chains 258 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 149 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.0050 chunk 81 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.0010 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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: 0.7710 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7846 Z= 0.205 Angle : 0.725 9.905 10652 Z= 0.370 Chirality : 0.043 0.153 1138 Planarity : 0.005 0.056 1296 Dihedral : 6.792 55.986 1070 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 4.34 % Allowed : 27.79 % Favored : 67.87 % 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: -0.41 (0.28), residues: 886 helix: 1.18 (0.21), residues: 552 sheet: -0.35 (0.67), residues: 56 loop : -3.41 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 68 HIS 0.004 0.001 HIS D 52 PHE 0.035 0.001 PHE A 158 TYR 0.019 0.001 TYR B 92 ARG 0.003 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8108 (pp) cc_final: 0.7899 (pp) REVERT: A 233 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: B 28 PHE cc_start: 0.8709 (t80) cc_final: 0.8435 (t80) REVERT: B 149 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.6281 (p90) REVERT: C 91 LEU cc_start: 0.8274 (pp) cc_final: 0.8051 (pp) REVERT: C 140 MET cc_start: 0.8467 (tpp) cc_final: 0.8243 (mtt) REVERT: C 248 ASP cc_start: 0.7841 (t0) cc_final: 0.6801 (t0) REVERT: C 251 GLU cc_start: 0.7341 (pm20) cc_final: 0.6804 (pm20) REVERT: C 342 ASN cc_start: 0.7364 (t0) cc_final: 0.7097 (t0) REVERT: C 346 GLN cc_start: 0.8150 (mp10) cc_final: 0.7901 (mp10) REVERT: D 28 PHE cc_start: 0.8552 (t80) cc_final: 0.8311 (t80) REVERT: D 92 TYR cc_start: 0.8182 (m-10) cc_final: 0.7730 (m-10) outliers start: 35 outliers final: 30 residues processed: 248 average time/residue: 0.1642 time to fit residues: 57.4111 Evaluate side-chains 252 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.7729 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7846 Z= 0.220 Angle : 0.751 9.860 10652 Z= 0.385 Chirality : 0.044 0.221 1138 Planarity : 0.005 0.052 1296 Dihedral : 6.746 56.047 1070 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.71 % Allowed : 28.41 % Favored : 66.87 % 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: -0.41 (0.28), residues: 886 helix: 1.18 (0.21), residues: 552 sheet: -0.32 (0.69), residues: 56 loop : -3.41 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 68 HIS 0.004 0.001 HIS D 52 PHE 0.029 0.002 PHE C 373 TYR 0.021 0.001 TYR D 92 ARG 0.004 0.000 ARG D 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8185 (pp) cc_final: 0.7978 (pp) REVERT: A 140 MET cc_start: 0.8621 (tpp) cc_final: 0.7935 (tpp) REVERT: A 182 TYR cc_start: 0.8197 (p90) cc_final: 0.7965 (p90) REVERT: A 233 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: A 251 GLU cc_start: 0.7626 (pm20) cc_final: 0.7221 (pm20) REVERT: B 28 PHE cc_start: 0.8719 (t80) cc_final: 0.8450 (t80) REVERT: B 149 HIS cc_start: 0.6858 (OUTLIER) cc_final: 0.6244 (p90) REVERT: C 140 MET cc_start: 0.8478 (tpp) cc_final: 0.8261 (mtt) REVERT: C 182 TYR cc_start: 0.8220 (p90) cc_final: 0.7996 (p90) REVERT: C 342 ASN cc_start: 0.7375 (t0) cc_final: 0.7114 (t0) REVERT: D 28 PHE cc_start: 0.8556 (t80) cc_final: 0.8324 (t80) REVERT: D 149 HIS cc_start: 0.7068 (OUTLIER) cc_final: 0.6484 (p90) outliers start: 38 outliers final: 32 residues processed: 245 average time/residue: 0.1606 time to fit residues: 55.9703 Evaluate side-chains 255 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 149 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.0270 chunk 71 optimal weight: 0.0270 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.138161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.116122 restraints weight = 17168.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.119329 restraints weight = 9919.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121500 restraints weight = 6881.667| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7846 Z= 0.206 Angle : 0.758 13.171 10652 Z= 0.384 Chirality : 0.043 0.187 1138 Planarity : 0.005 0.055 1296 Dihedral : 6.573 56.221 1070 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.22 % Allowed : 30.40 % Favored : 65.38 % 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: -0.30 (0.28), residues: 886 helix: 1.26 (0.21), residues: 552 sheet: -0.14 (0.72), residues: 56 loop : -3.38 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 68 HIS 0.003 0.001 HIS D 52 PHE 0.030 0.001 PHE C 373 TYR 0.019 0.001 TYR B 42 ARG 0.005 0.000 ARG D 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1907.86 seconds wall clock time: 35 minutes 44.70 seconds (2144.70 seconds total)