Starting phenix.real_space_refine on Sun Mar 10 23:20:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/03_2024/8uyi_42807_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/03_2024/8uyi_42807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/03_2024/8uyi_42807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/03_2024/8uyi_42807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/03_2024/8uyi_42807_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/03_2024/8uyi_42807_updated.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 P 8 5.49 5 Mg 4 5.21 5 S 40 5.16 5 C 3804 2.51 5 N 1003 2.21 5 O 1121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 358": "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: 5980 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2966 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'TPO:plan-1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2956 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain breaks: 6 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.93, per 1000 atoms: 0.66 Number of scatterers: 5980 At special positions: 0 Unit cell: (116.352, 74.336, 72.72, 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) S 40 16.00 P 8 15.00 Mg 4 11.99 O 1121 8.00 N 1003 7.00 C 3804 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: 2.54 Conformation dependent library (CDL) restraints added in 1.3 seconds 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 7 sheets defined 38.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 389 through 392 No H-bonds generated for 'chain 'A' and resid 389 through 392' Processing helix chain 'A' and resid 407 through 419 removed outlier: 4.042A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.578A pdb=" N SER A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 499 through 514 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.660A pdb=" N GLU B 133 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 136 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 137 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 204 through 217 removed outlier: 3.546A pdb=" N THR B 215 " --> pdb=" O MET B 211 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Proline residue: B 217 - end of helix Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.564A pdb=" N ARG B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 389 through 392 No H-bonds generated for 'chain 'B' and resid 389 through 392' Processing helix chain 'B' and resid 407 through 419 removed outlier: 3.522A pdb=" N ALA B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 removed outlier: 3.556A pdb=" N SER B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 499 through 514 removed outlier: 3.624A pdb=" N LYS B 512 " --> pdb=" O CYS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 558 through 573 Processing sheet with id= A, first strand: chain 'A' and resid 249 through 254 removed outlier: 6.944A pdb=" N VAL A 289 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 252 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE A 287 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA A 254 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER A 285 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER A 175 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 340 through 343 Processing sheet with id= C, first strand: chain 'A' and resid 370 through 372 Processing sheet with id= D, first strand: chain 'B' and resid 159 through 161 removed outlier: 3.664A pdb=" N SER B 251 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS B 291 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET B 249 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER B 220 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 340 through 343 Processing sheet with id= F, first strand: chain 'B' and resid 370 through 372 Processing sheet with id= G, first strand: chain 'B' and resid 164 through 167 removed outlier: 6.837A pdb=" N VAL B 173 " --> pdb=" O ILE B 165 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 621 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: 1.54 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1895 1.34 - 1.46: 1213 1.46 - 1.58: 2905 1.58 - 1.69: 20 1.69 - 1.81: 62 Bond restraints: 6095 Sorted by residual: bond pdb=" OG1 TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.84e+01 bond pdb=" OG1 TPO B 305 " pdb=" P TPO B 305 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O2P TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O3P TPO B 305 " pdb=" P TPO B 305 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O3P TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 6090 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.92: 161 105.92 - 113.47: 3426 113.47 - 121.02: 2927 121.02 - 128.57: 1703 128.57 - 136.12: 48 Bond angle restraints: 8265 Sorted by residual: angle pdb=" CB TPO A 305 " pdb=" OG1 TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 119.31 107.32 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C THR B 215 " pdb=" N VAL B 216 " pdb=" CA VAL B 216 " ideal model delta sigma weight residual 120.33 123.43 -3.10 8.00e-01 1.56e+00 1.50e+01 angle pdb=" CB TPO B 305 " pdb=" OG1 TPO B 305 " pdb=" P TPO B 305 " ideal model delta sigma weight residual 119.31 108.58 10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" OG1 TPO B 305 " pdb=" P TPO B 305 " pdb=" O1P TPO B 305 " ideal model delta sigma weight residual 100.43 111.06 -10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" OG1 TPO A 305 " pdb=" P TPO A 305 " pdb=" O1P TPO A 305 " ideal model delta sigma weight residual 100.43 110.11 -9.68 3.00e+00 1.11e-01 1.04e+01 ... (remaining 8260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.23: 3638 33.23 - 66.46: 60 66.46 - 99.69: 2 99.69 - 132.91: 0 132.91 - 166.14: 2 Dihedral angle restraints: 3702 sinusoidal: 1516 harmonic: 2186 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 133.86 166.14 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 89.85 -149.86 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 24.11 -84.11 1 2.00e+01 2.50e-03 2.15e+01 ... (remaining 3699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 597 0.031 - 0.062: 220 0.062 - 0.093: 69 0.093 - 0.124: 38 0.124 - 0.155: 8 Chirality restraints: 932 Sorted by residual: chirality pdb=" CA ILE A 450 " pdb=" N ILE A 450 " pdb=" C ILE A 450 " pdb=" CB ILE A 450 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA ILE A 246 " pdb=" N ILE A 246 " pdb=" C ILE A 246 " pdb=" CB ILE A 246 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE B 246 " pdb=" N ILE B 246 " pdb=" C ILE B 246 " pdb=" CB ILE B 246 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 929 not shown) Planarity restraints: 1029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 243 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO A 244 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 244 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 244 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 243 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO B 244 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 244 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 244 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 450 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO B 451 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " -0.021 5.00e-02 4.00e+02 ... (remaining 1026 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 70 2.63 - 3.19: 4836 3.19 - 3.76: 8977 3.76 - 4.33: 13083 4.33 - 4.90: 21255 Nonbonded interactions: 48221 Sorted by model distance: nonbonded pdb=" O2A ADP B 601 " pdb="MG MG B 603 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP B 357 " pdb="MG MG B 602 " model vdw 2.073 2.170 nonbonded pdb=" OD1 ASN A 339 " pdb="MG MG A 603 " model vdw 2.105 2.170 nonbonded pdb=" OD1 ASN B 339 " pdb="MG MG B 603 " model vdw 2.205 2.170 nonbonded pdb=" OD2 ASP A 357 " pdb="MG MG A 603 " model vdw 2.240 2.170 ... (remaining 48216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 122 through 223 or resid 237 through 572 or resid 601 thro \ ugh 603)) selection = (chain 'B' and (resid 122 through 136 or resid 148 through 572 or resid 601 thro \ ugh 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 3.810 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.960 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 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 : 0.004 0.106 6095 Z= 0.262 Angle : 0.673 11.987 8265 Z= 0.341 Chirality : 0.041 0.155 932 Planarity : 0.005 0.043 1029 Dihedral : 12.678 166.142 2272 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.08 % Allowed : 4.92 % Favored : 94.00 % 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 (0.29), residues: 698 helix: -0.70 (0.24), residues: 299 sheet: -0.09 (0.56), residues: 92 loop : -0.35 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 489 HIS 0.003 0.001 HIS A 243 PHE 0.011 0.001 PHE A 253 TYR 0.007 0.001 TYR B 438 ARG 0.003 0.001 ARG B 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7676 (mt) cc_final: 0.7309 (mm) REVERT: A 194 MET cc_start: 0.8047 (ttt) cc_final: 0.7398 (tmm) REVERT: A 197 ASN cc_start: 0.8029 (t0) cc_final: 0.7664 (t0) REVERT: A 219 MET cc_start: 0.8061 (mtt) cc_final: 0.7833 (mtt) REVERT: A 236 PHE cc_start: 0.5701 (m-80) cc_final: 0.5054 (m-80) REVERT: A 318 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7616 (tt) REVERT: A 334 ASP cc_start: 0.7492 (t70) cc_final: 0.7116 (t0) REVERT: A 433 LEU cc_start: 0.8041 (mt) cc_final: 0.7794 (mp) REVERT: A 436 LYS cc_start: 0.7240 (tttt) cc_final: 0.6742 (ttpt) REVERT: A 452 PHE cc_start: 0.7155 (t80) cc_final: 0.6787 (t80) REVERT: A 456 ASN cc_start: 0.8273 (m-40) cc_final: 0.7861 (m-40) REVERT: A 558 LEU cc_start: 0.7429 (tp) cc_final: 0.7100 (tp) REVERT: B 129 TRP cc_start: 0.7335 (t60) cc_final: 0.6833 (t60) REVERT: B 298 LYS cc_start: 0.7700 (tttt) cc_final: 0.7418 (ttpt) REVERT: B 377 ASP cc_start: 0.5506 (t70) cc_final: 0.5239 (t0) REVERT: B 393 ASN cc_start: 0.7864 (m-40) cc_final: 0.7141 (m110) REVERT: B 401 TRP cc_start: 0.7061 (m100) cc_final: 0.6809 (m-90) REVERT: B 403 ASN cc_start: 0.8165 (t0) cc_final: 0.7454 (p0) REVERT: B 418 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7227 (tt0) REVERT: B 436 LYS cc_start: 0.6073 (tttt) cc_final: 0.4809 (mptt) REVERT: B 439 LYS cc_start: 0.7546 (mttt) cc_final: 0.7313 (mtpt) REVERT: B 442 ASP cc_start: 0.8205 (m-30) cc_final: 0.7741 (m-30) REVERT: B 471 ASP cc_start: 0.7209 (m-30) cc_final: 0.6912 (m-30) REVERT: B 501 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7540 (mt-10) REVERT: B 541 ARG cc_start: 0.5720 (mtt-85) cc_final: 0.5463 (mtm-85) REVERT: B 566 LYS cc_start: 0.8027 (tttt) cc_final: 0.7765 (ttpp) outliers start: 7 outliers final: 2 residues processed: 199 average time/residue: 0.2060 time to fit residues: 51.8573 Evaluate side-chains 145 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 0.0060 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN B 328 HIS B 504 GLN B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6095 Z= 0.164 Angle : 0.543 6.133 8265 Z= 0.259 Chirality : 0.039 0.131 932 Planarity : 0.004 0.035 1029 Dihedral : 9.642 141.486 827 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.92 % Allowed : 10.92 % Favored : 86.15 % 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 (0.31), residues: 698 helix: 0.87 (0.28), residues: 302 sheet: -0.51 (0.49), residues: 106 loop : 0.13 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.012 0.002 HIS A 559 PHE 0.006 0.001 PHE B 399 TYR 0.015 0.001 TYR A 174 ARG 0.002 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7639 (mt) cc_final: 0.7278 (mm) REVERT: A 194 MET cc_start: 0.7803 (ttt) cc_final: 0.7318 (tmm) REVERT: A 204 SER cc_start: 0.7896 (OUTLIER) cc_final: 0.7574 (m) REVERT: A 219 MET cc_start: 0.8018 (mtt) cc_final: 0.7814 (mtt) REVERT: A 236 PHE cc_start: 0.5777 (m-80) cc_final: 0.5236 (m-80) REVERT: A 299 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7158 (pt0) REVERT: A 318 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7327 (tt) REVERT: A 320 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6941 (mm-30) REVERT: A 334 ASP cc_start: 0.7450 (t70) cc_final: 0.6548 (t0) REVERT: A 418 GLU cc_start: 0.5773 (mt-10) cc_final: 0.5188 (mt-10) REVERT: A 433 LEU cc_start: 0.8008 (mt) cc_final: 0.7752 (mp) REVERT: A 436 LYS cc_start: 0.7164 (tttt) cc_final: 0.6698 (ttpt) REVERT: A 456 ASN cc_start: 0.8138 (m-40) cc_final: 0.7836 (m110) REVERT: B 129 TRP cc_start: 0.6983 (t60) cc_final: 0.6699 (t60) REVERT: B 213 ARG cc_start: 0.7646 (mtt180) cc_final: 0.6995 (mtt-85) REVERT: B 401 TRP cc_start: 0.7099 (m100) cc_final: 0.6819 (m-90) REVERT: B 403 ASN cc_start: 0.8121 (t0) cc_final: 0.7504 (p0) REVERT: B 436 LYS cc_start: 0.6130 (tttt) cc_final: 0.4903 (mptt) REVERT: B 541 ARG cc_start: 0.5863 (mtt-85) cc_final: 0.5502 (mtm-85) REVERT: B 547 GLU cc_start: 0.6978 (tp30) cc_final: 0.6393 (tm-30) REVERT: B 566 LYS cc_start: 0.8008 (tttt) cc_final: 0.7696 (ttpp) outliers start: 19 outliers final: 10 residues processed: 159 average time/residue: 0.1878 time to fit residues: 38.3466 Evaluate side-chains 145 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 54 optimal weight: 0.0970 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS B 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6095 Z= 0.187 Angle : 0.544 6.281 8265 Z= 0.255 Chirality : 0.040 0.129 932 Planarity : 0.004 0.034 1029 Dihedral : 8.751 125.931 824 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.62 % Allowed : 12.31 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.32), residues: 698 helix: 1.53 (0.30), residues: 299 sheet: -0.60 (0.48), residues: 114 loop : 0.19 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.010 0.002 HIS A 559 PHE 0.012 0.001 PHE B 399 TYR 0.015 0.001 TYR A 350 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 0.777 Fit side-chains REVERT: A 158 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: A 161 LEU cc_start: 0.7661 (mt) cc_final: 0.7298 (mm) REVERT: A 194 MET cc_start: 0.7936 (ttt) cc_final: 0.7520 (tmm) REVERT: A 236 PHE cc_start: 0.5793 (m-80) cc_final: 0.5357 (m-80) REVERT: A 318 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7364 (tt) REVERT: A 320 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6806 (mm-30) REVERT: A 334 ASP cc_start: 0.7506 (t70) cc_final: 0.6621 (t0) REVERT: A 418 GLU cc_start: 0.5836 (mt-10) cc_final: 0.5069 (mt-10) REVERT: A 433 LEU cc_start: 0.8019 (mt) cc_final: 0.7748 (mp) REVERT: A 436 LYS cc_start: 0.7139 (tttt) cc_final: 0.6670 (ttpt) REVERT: A 439 LYS cc_start: 0.7114 (mttt) cc_final: 0.6572 (tttp) REVERT: A 456 ASN cc_start: 0.8176 (m-40) cc_final: 0.7954 (m110) REVERT: A 570 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7505 (tt0) REVERT: B 213 ARG cc_start: 0.7761 (mtt180) cc_final: 0.7078 (mtt-85) REVERT: B 249 MET cc_start: 0.8213 (ttm) cc_final: 0.7678 (ttm) REVERT: B 401 TRP cc_start: 0.7170 (m100) cc_final: 0.6860 (m-90) REVERT: B 403 ASN cc_start: 0.8149 (t0) cc_final: 0.7498 (p0) REVERT: B 436 LYS cc_start: 0.6163 (tttt) cc_final: 0.4871 (mptt) REVERT: B 541 ARG cc_start: 0.5843 (mtt-85) cc_final: 0.5459 (mtm-85) REVERT: B 547 GLU cc_start: 0.7086 (tp30) cc_final: 0.6489 (tm-30) REVERT: B 566 LYS cc_start: 0.7998 (tttt) cc_final: 0.7577 (ttpp) outliers start: 17 outliers final: 12 residues processed: 143 average time/residue: 0.1992 time to fit residues: 36.6805 Evaluate side-chains 143 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 326 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6095 Z= 0.152 Angle : 0.539 13.196 8265 Z= 0.248 Chirality : 0.039 0.130 932 Planarity : 0.004 0.034 1029 Dihedral : 7.940 116.059 824 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.08 % Allowed : 13.23 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.33), residues: 698 helix: 1.76 (0.31), residues: 298 sheet: -0.59 (0.47), residues: 114 loop : 0.27 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.012 0.001 HIS A 559 PHE 0.006 0.001 PHE A 253 TYR 0.018 0.001 TYR A 350 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 0.761 Fit side-chains REVERT: A 158 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6882 (mp0) REVERT: A 161 LEU cc_start: 0.7643 (mt) cc_final: 0.7276 (mm) REVERT: A 194 MET cc_start: 0.7896 (ttt) cc_final: 0.7455 (tmm) REVERT: A 221 TYR cc_start: 0.7963 (m-80) cc_final: 0.7726 (m-80) REVERT: A 236 PHE cc_start: 0.5941 (m-80) cc_final: 0.5562 (m-80) REVERT: A 249 MET cc_start: 0.7569 (ttm) cc_final: 0.7368 (mtp) REVERT: A 318 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7342 (tt) REVERT: A 320 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6810 (mm-30) REVERT: A 334 ASP cc_start: 0.7512 (t70) cc_final: 0.6619 (t0) REVERT: A 433 LEU cc_start: 0.7990 (mt) cc_final: 0.7716 (mp) REVERT: A 436 LYS cc_start: 0.7142 (tttt) cc_final: 0.6669 (ttpt) REVERT: A 439 LYS cc_start: 0.7137 (mttt) cc_final: 0.6636 (tttp) REVERT: A 456 ASN cc_start: 0.8139 (m-40) cc_final: 0.7935 (m110) REVERT: A 570 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7584 (tt0) REVERT: B 213 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7064 (mtt-85) REVERT: B 249 MET cc_start: 0.8121 (ttm) cc_final: 0.7698 (ttm) REVERT: B 401 TRP cc_start: 0.7174 (m100) cc_final: 0.6809 (m-90) REVERT: B 403 ASN cc_start: 0.8145 (t0) cc_final: 0.7479 (p0) REVERT: B 436 LYS cc_start: 0.6161 (tttt) cc_final: 0.4855 (mptt) REVERT: B 440 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7486 (mp0) REVERT: B 541 ARG cc_start: 0.5860 (mtt-85) cc_final: 0.5479 (mtm-85) REVERT: B 547 GLU cc_start: 0.7085 (tp30) cc_final: 0.6481 (tm-30) REVERT: B 573 ILE cc_start: 0.7316 (mt) cc_final: 0.7049 (pt) outliers start: 20 outliers final: 17 residues processed: 148 average time/residue: 0.2017 time to fit residues: 38.3465 Evaluate side-chains 143 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6095 Z= 0.170 Angle : 0.547 14.778 8265 Z= 0.249 Chirality : 0.039 0.127 932 Planarity : 0.004 0.034 1029 Dihedral : 7.658 114.175 824 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.85 % Allowed : 13.54 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.33), residues: 698 helix: 1.88 (0.31), residues: 297 sheet: -0.58 (0.48), residues: 114 loop : 0.27 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.008 0.001 HIS A 559 PHE 0.006 0.001 PHE B 253 TYR 0.015 0.001 TYR A 482 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.728 Fit side-chains REVERT: A 157 ASP cc_start: 0.7646 (p0) cc_final: 0.7153 (p0) REVERT: A 158 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: A 161 LEU cc_start: 0.7752 (mt) cc_final: 0.7383 (mm) REVERT: A 194 MET cc_start: 0.7787 (ttt) cc_final: 0.7335 (tmm) REVERT: A 236 PHE cc_start: 0.5870 (m-80) cc_final: 0.5545 (m-80) REVERT: A 318 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7387 (tt) REVERT: A 320 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6825 (mm-30) REVERT: A 334 ASP cc_start: 0.7566 (t70) cc_final: 0.7139 (t0) REVERT: A 433 LEU cc_start: 0.8005 (mt) cc_final: 0.7722 (mp) REVERT: A 436 LYS cc_start: 0.7112 (tttt) cc_final: 0.6660 (ttpt) REVERT: A 439 LYS cc_start: 0.7109 (mttt) cc_final: 0.6620 (tttp) REVERT: A 570 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7571 (tt0) REVERT: B 213 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7130 (mtt-85) REVERT: B 249 MET cc_start: 0.8111 (ttm) cc_final: 0.7763 (ttm) REVERT: B 401 TRP cc_start: 0.7258 (m100) cc_final: 0.6859 (m-90) REVERT: B 403 ASN cc_start: 0.8111 (t0) cc_final: 0.7435 (p0) REVERT: B 436 LYS cc_start: 0.6223 (tttt) cc_final: 0.4896 (mptt) REVERT: B 541 ARG cc_start: 0.5921 (mtt-85) cc_final: 0.5522 (mtm-85) REVERT: B 547 GLU cc_start: 0.7129 (tp30) cc_final: 0.6508 (tm-30) outliers start: 25 outliers final: 18 residues processed: 144 average time/residue: 0.1871 time to fit residues: 35.1647 Evaluate side-chains 146 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6095 Z= 0.129 Angle : 0.527 15.060 8265 Z= 0.238 Chirality : 0.038 0.128 932 Planarity : 0.003 0.033 1029 Dihedral : 7.418 111.889 824 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.08 % Allowed : 13.54 % Favored : 83.38 % 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: 1.30 (0.33), residues: 698 helix: 2.02 (0.31), residues: 298 sheet: -0.49 (0.48), residues: 114 loop : 0.33 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 129 HIS 0.009 0.001 HIS A 559 PHE 0.006 0.001 PHE B 287 TYR 0.016 0.001 TYR A 494 ARG 0.001 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.753 Fit side-chains REVERT: A 161 LEU cc_start: 0.7781 (mt) cc_final: 0.7409 (mm) REVERT: A 194 MET cc_start: 0.7686 (ttt) cc_final: 0.7260 (tmm) REVERT: A 221 TYR cc_start: 0.7891 (m-80) cc_final: 0.7531 (m-80) REVERT: A 318 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7344 (tt) REVERT: A 320 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 334 ASP cc_start: 0.7523 (t70) cc_final: 0.7111 (t0) REVERT: A 436 LYS cc_start: 0.7136 (tttt) cc_final: 0.6644 (ttpt) REVERT: A 439 LYS cc_start: 0.7080 (mttt) cc_final: 0.6603 (tttp) REVERT: A 570 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7628 (tt0) REVERT: B 213 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7128 (mtt-85) REVERT: B 401 TRP cc_start: 0.7288 (m100) cc_final: 0.6824 (m-90) REVERT: B 403 ASN cc_start: 0.8083 (t0) cc_final: 0.7396 (p0) REVERT: B 436 LYS cc_start: 0.6132 (tttt) cc_final: 0.4807 (mptt) REVERT: B 441 GLU cc_start: 0.7805 (pm20) cc_final: 0.7440 (pm20) REVERT: B 541 ARG cc_start: 0.5818 (mtt-85) cc_final: 0.5491 (mtm-85) REVERT: B 547 GLU cc_start: 0.7144 (tp30) cc_final: 0.6515 (tm-30) outliers start: 20 outliers final: 16 residues processed: 144 average time/residue: 0.1830 time to fit residues: 34.1583 Evaluate side-chains 138 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6095 Z= 0.168 Angle : 0.551 15.855 8265 Z= 0.250 Chirality : 0.039 0.128 932 Planarity : 0.003 0.033 1029 Dihedral : 7.370 111.528 824 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.69 % Allowed : 13.38 % Favored : 82.92 % 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: 1.32 (0.33), residues: 698 helix: 1.98 (0.31), residues: 297 sheet: -0.52 (0.48), residues: 112 loop : 0.42 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.003 0.001 HIS A 243 PHE 0.010 0.001 PHE A 452 TYR 0.016 0.001 TYR A 494 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.738 Fit side-chains REVERT: A 161 LEU cc_start: 0.7804 (mt) cc_final: 0.7443 (mm) REVERT: A 194 MET cc_start: 0.7737 (ttt) cc_final: 0.7290 (tmm) REVERT: A 221 TYR cc_start: 0.7897 (m-80) cc_final: 0.7572 (m-80) REVERT: A 318 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7383 (tt) REVERT: A 320 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6794 (mm-30) REVERT: A 334 ASP cc_start: 0.7591 (t70) cc_final: 0.7159 (t0) REVERT: A 439 LYS cc_start: 0.7028 (mttt) cc_final: 0.6549 (tttp) REVERT: A 570 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7689 (tt0) REVERT: B 213 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7352 (mtt-85) REVERT: B 401 TRP cc_start: 0.7314 (m100) cc_final: 0.6884 (m-90) REVERT: B 436 LYS cc_start: 0.6166 (tttt) cc_final: 0.4833 (mptt) REVERT: B 541 ARG cc_start: 0.5755 (mtt-85) cc_final: 0.5391 (mtm-85) REVERT: B 547 GLU cc_start: 0.7114 (tp30) cc_final: 0.6485 (tm-30) REVERT: B 573 ILE cc_start: 0.6080 (tp) cc_final: 0.5788 (pt) outliers start: 24 outliers final: 22 residues processed: 141 average time/residue: 0.1873 time to fit residues: 34.4427 Evaluate side-chains 144 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 6095 Z= 0.140 Angle : 0.535 16.370 8265 Z= 0.242 Chirality : 0.038 0.128 932 Planarity : 0.003 0.033 1029 Dihedral : 7.238 109.144 824 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.92 % Allowed : 13.85 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.33), residues: 698 helix: 2.10 (0.31), residues: 296 sheet: -0.50 (0.47), residues: 112 loop : 0.50 (0.40), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.002 0.000 HIS A 243 PHE 0.009 0.001 PHE A 452 TYR 0.015 0.001 TYR A 494 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.717 Fit side-chains REVERT: A 157 ASP cc_start: 0.7592 (p0) cc_final: 0.7059 (p0) REVERT: A 158 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: A 161 LEU cc_start: 0.7780 (mt) cc_final: 0.7426 (mm) REVERT: A 194 MET cc_start: 0.7650 (ttt) cc_final: 0.7224 (tmm) REVERT: A 221 TYR cc_start: 0.7909 (m-80) cc_final: 0.7579 (m-80) REVERT: A 318 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7361 (tt) REVERT: A 320 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 334 ASP cc_start: 0.7558 (t70) cc_final: 0.7139 (t0) REVERT: A 377 ASP cc_start: 0.7659 (m-30) cc_final: 0.7312 (t0) REVERT: A 439 LYS cc_start: 0.7025 (mttt) cc_final: 0.6578 (tttp) REVERT: A 570 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7675 (tt0) REVERT: B 213 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7237 (mtt-85) REVERT: B 401 TRP cc_start: 0.7331 (m100) cc_final: 0.6872 (m-90) REVERT: B 436 LYS cc_start: 0.6090 (tttt) cc_final: 0.4744 (mptt) REVERT: B 541 ARG cc_start: 0.5872 (mtt-85) cc_final: 0.5522 (mtm-85) REVERT: B 547 GLU cc_start: 0.7160 (tp30) cc_final: 0.6537 (tm-30) REVERT: B 573 ILE cc_start: 0.6097 (tp) cc_final: 0.5824 (pt) outliers start: 19 outliers final: 16 residues processed: 134 average time/residue: 0.1864 time to fit residues: 32.4886 Evaluate side-chains 138 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6095 Z= 0.159 Angle : 0.548 16.399 8265 Z= 0.248 Chirality : 0.039 0.130 932 Planarity : 0.003 0.033 1029 Dihedral : 7.200 107.265 824 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.69 % Allowed : 13.85 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.33), residues: 698 helix: 2.05 (0.31), residues: 296 sheet: -0.49 (0.48), residues: 112 loop : 0.50 (0.40), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.003 0.001 HIS A 243 PHE 0.019 0.001 PHE A 452 TYR 0.015 0.001 TYR A 494 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 0.756 Fit side-chains REVERT: A 161 LEU cc_start: 0.7775 (mt) cc_final: 0.7434 (mm) REVERT: A 194 MET cc_start: 0.7704 (ttt) cc_final: 0.7277 (tmm) REVERT: A 221 TYR cc_start: 0.7895 (m-80) cc_final: 0.7525 (m-80) REVERT: A 290 MET cc_start: 0.8545 (mtm) cc_final: 0.8312 (mtm) REVERT: A 318 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7371 (tt) REVERT: A 320 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6838 (mm-30) REVERT: A 334 ASP cc_start: 0.7597 (t70) cc_final: 0.7163 (t0) REVERT: A 377 ASP cc_start: 0.7706 (m-30) cc_final: 0.7378 (t0) REVERT: A 439 LYS cc_start: 0.6996 (mttt) cc_final: 0.6524 (tttp) REVERT: A 570 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7696 (tt0) REVERT: B 213 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7246 (mtt-85) REVERT: B 401 TRP cc_start: 0.7347 (m100) cc_final: 0.6881 (m-90) REVERT: B 436 LYS cc_start: 0.6127 (tttt) cc_final: 0.4784 (mptt) REVERT: B 541 ARG cc_start: 0.5771 (mtt-85) cc_final: 0.5321 (mtm-85) REVERT: B 547 GLU cc_start: 0.7184 (tp30) cc_final: 0.6552 (tm-30) REVERT: B 573 ILE cc_start: 0.6028 (tp) cc_final: 0.5776 (pt) outliers start: 24 outliers final: 20 residues processed: 140 average time/residue: 0.1836 time to fit residues: 33.5287 Evaluate side-chains 144 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6095 Z= 0.159 Angle : 0.550 16.585 8265 Z= 0.250 Chirality : 0.039 0.154 932 Planarity : 0.003 0.033 1029 Dihedral : 7.166 105.301 824 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.54 % Allowed : 14.31 % Favored : 82.15 % 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: 1.40 (0.33), residues: 698 helix: 2.06 (0.31), residues: 296 sheet: -0.22 (0.50), residues: 102 loop : 0.32 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 129 HIS 0.003 0.001 HIS A 243 PHE 0.008 0.001 PHE A 452 TYR 0.014 0.001 TYR A 494 ARG 0.002 0.000 ARG B 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.686 Fit side-chains REVERT: A 161 LEU cc_start: 0.7765 (mt) cc_final: 0.7421 (mm) REVERT: A 194 MET cc_start: 0.7620 (ttt) cc_final: 0.7209 (tmm) REVERT: A 221 TYR cc_start: 0.7858 (m-80) cc_final: 0.7517 (m-80) REVERT: A 249 MET cc_start: 0.7659 (mtp) cc_final: 0.7456 (ttm) REVERT: A 290 MET cc_start: 0.8559 (mtm) cc_final: 0.8337 (mtm) REVERT: A 318 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7368 (tt) REVERT: A 320 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6835 (mm-30) REVERT: A 334 ASP cc_start: 0.7569 (t70) cc_final: 0.7140 (t0) REVERT: A 377 ASP cc_start: 0.7712 (m-30) cc_final: 0.7378 (t0) REVERT: A 439 LYS cc_start: 0.7015 (mttt) cc_final: 0.6565 (tttp) REVERT: A 570 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7700 (tt0) REVERT: B 401 TRP cc_start: 0.7342 (m100) cc_final: 0.6866 (m-90) REVERT: B 436 LYS cc_start: 0.6109 (tttt) cc_final: 0.4760 (mptt) REVERT: B 440 GLU cc_start: 0.7755 (mt-10) cc_final: 0.6854 (mt-10) REVERT: B 541 ARG cc_start: 0.5845 (mtt-85) cc_final: 0.5451 (mtm-85) REVERT: B 547 GLU cc_start: 0.7223 (tp30) cc_final: 0.6575 (tm-30) REVERT: B 573 ILE cc_start: 0.6084 (tp) cc_final: 0.5833 (pt) outliers start: 23 outliers final: 22 residues processed: 138 average time/residue: 0.1868 time to fit residues: 33.3673 Evaluate side-chains 146 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.188682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165279 restraints weight = 6969.215| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.94 r_work: 0.3762 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6095 Z= 0.207 Angle : 0.578 16.619 8265 Z= 0.263 Chirality : 0.040 0.131 932 Planarity : 0.004 0.033 1029 Dihedral : 7.242 102.839 824 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.54 % Allowed : 14.31 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.33), residues: 698 helix: 1.88 (0.31), residues: 297 sheet: -0.29 (0.51), residues: 102 loop : 0.29 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.010 0.001 HIS A 559 PHE 0.017 0.001 PHE A 452 TYR 0.015 0.001 TYR A 482 ARG 0.004 0.000 ARG B 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1804.77 seconds wall clock time: 33 minutes 28.14 seconds (2008.14 seconds total)