Starting phenix.real_space_refine on Wed Mar 12 01:32:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chu_45602/03_2025/9chu_45602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chu_45602/03_2025/9chu_45602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9chu_45602/03_2025/9chu_45602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chu_45602/03_2025/9chu_45602.map" model { file = "/net/cci-nas-00/data/ceres_data/9chu_45602/03_2025/9chu_45602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chu_45602/03_2025/9chu_45602.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4555 2.51 5 N 1151 2.21 5 O 1255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7009 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3326 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 9, 'TRANS': 418} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2806 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLU%COO:oxt': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'FK5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.37, per 1000 atoms: 0.77 Number of scatterers: 7009 At special positions: 0 Unit cell: (64.6, 84.15, 152.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1255 8.00 N 1151 7.00 C 4555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 190 " 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: 1.69 Conformation dependent library (CDL) restraints added in 963.1 milliseconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 52.3% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 removed outlier: 3.891A pdb=" N PHE A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 97 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 102 through 137 removed outlier: 3.543A pdb=" N CYS A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 146 through 171 Proline residue: A 168 - end of helix removed outlier: 3.522A pdb=" N MET A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.581A pdb=" N VAL A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.736A pdb=" N ILE A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.561A pdb=" N ILE A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.797A pdb=" N LEU A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 395 through 421 Proline residue: A 411 - end of helix removed outlier: 4.711A pdb=" N ILE A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.536A pdb=" N ASN A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 removed outlier: 4.183A pdb=" N LEU A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 56 through 73 removed outlier: 3.829A pdb=" N GLN B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 4.194A pdb=" N LYS B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.713A pdb=" N GLU B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.719A pdb=" N TYR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 347 through 368 Proline residue: B 354 - end of helix Processing helix chain 'C' and resid 56 through 61 Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.142A pdb=" N LEU B 195 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 276 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE B 304 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG B 278 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.591A pdb=" N LEU B 113 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 112 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 324 Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.607A pdb=" N THR C 21 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 106 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL C 23 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 35 through 38 removed outlier: 6.549A pdb=" N LYS C 35 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 37 " --> pdb=" O GLY C 28 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 942 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: 1.84 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1848 1.33 - 1.45: 1331 1.45 - 1.57: 3925 1.57 - 1.69: 1 1.69 - 1.81: 73 Bond restraints: 7178 Sorted by residual: bond pdb=" CA SER A 204 " pdb=" CB SER A 204 " ideal model delta sigma weight residual 1.528 1.424 0.104 1.56e-02 4.11e+03 4.49e+01 bond pdb=" CA SER A 203 " pdb=" CB SER A 203 " ideal model delta sigma weight residual 1.529 1.440 0.089 1.62e-02 3.81e+03 3.01e+01 bond pdb=" CA SER A 207 " pdb=" CB SER A 207 " ideal model delta sigma weight residual 1.534 1.447 0.087 1.79e-02 3.12e+03 2.38e+01 bond pdb=" CAJ E5E A 501 " pdb=" OAC E5E A 501 " ideal model delta sigma weight residual 1.350 1.429 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" N ILE A 205 " pdb=" CA ILE A 205 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.25e-02 6.40e+03 1.47e+01 ... (remaining 7173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 9481 2.32 - 4.64: 210 4.64 - 6.95: 35 6.95 - 9.27: 13 9.27 - 11.59: 4 Bond angle restraints: 9743 Sorted by residual: angle pdb=" N VAL A 206 " pdb=" CA VAL A 206 " pdb=" C VAL A 206 " ideal model delta sigma weight residual 113.20 101.61 11.59 9.60e-01 1.09e+00 1.46e+02 angle pdb=" N VAL A 420 " pdb=" CA VAL A 420 " pdb=" C VAL A 420 " ideal model delta sigma weight residual 110.30 103.53 6.77 9.70e-01 1.06e+00 4.87e+01 angle pdb=" N ASP A 423 " pdb=" CA ASP A 423 " pdb=" C ASP A 423 " ideal model delta sigma weight residual 111.33 103.40 7.93 1.21e+00 6.83e-01 4.30e+01 angle pdb=" N SER A 203 " pdb=" CA SER A 203 " pdb=" CB SER A 203 " ideal model delta sigma weight residual 110.20 119.73 -9.53 1.49e+00 4.50e-01 4.09e+01 angle pdb=" N GLN A 422 " pdb=" CA GLN A 422 " pdb=" C GLN A 422 " ideal model delta sigma weight residual 113.15 105.90 7.25 1.19e+00 7.06e-01 3.71e+01 ... (remaining 9738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3812 17.65 - 35.30: 356 35.30 - 52.95: 72 52.95 - 70.60: 7 70.60 - 88.25: 5 Dihedral angle restraints: 4252 sinusoidal: 1673 harmonic: 2579 Sorted by residual: dihedral pdb=" CB CYS A 106 " pdb=" SG CYS A 106 " pdb=" SG CYS A 191 " pdb=" CB CYS A 191 " ideal model delta sinusoidal sigma weight residual -86.00 -174.25 88.25 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" N SER A 203 " pdb=" C SER A 203 " pdb=" CA SER A 203 " pdb=" CB SER A 203 " ideal model delta harmonic sigma weight residual 122.80 137.79 -14.99 0 2.50e+00 1.60e-01 3.60e+01 dihedral pdb=" C ARG A 175 " pdb=" N ARG A 175 " pdb=" CA ARG A 175 " pdb=" CB ARG A 175 " ideal model delta harmonic sigma weight residual -122.60 -136.04 13.44 0 2.50e+00 1.60e-01 2.89e+01 ... (remaining 4249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1079 0.132 - 0.264: 17 0.264 - 0.396: 3 0.396 - 0.529: 2 0.529 - 0.661: 1 Chirality restraints: 1102 Sorted by residual: chirality pdb=" CA SER A 203 " pdb=" N SER A 203 " pdb=" C SER A 203 " pdb=" CB SER A 203 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA ARG A 175 " pdb=" N ARG A 175 " pdb=" C ARG A 175 " pdb=" CB ARG A 175 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CAL E5E A 501 " pdb=" CAH E5E A 501 " pdb=" CAK E5E A 501 " pdb=" OAD E5E A 501 " both_signs ideal model delta sigma weight residual False -2.31 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1099 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 430 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C VAL A 430 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL A 430 " -0.025 2.00e-02 2.50e+03 pdb=" N TYR A 431 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 205 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ILE A 205 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE A 205 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 206 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 204 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.83e+00 pdb=" C SER A 204 " 0.051 2.00e-02 2.50e+03 pdb=" O SER A 204 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE A 205 " -0.018 2.00e-02 2.50e+03 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 282 2.71 - 3.26: 7155 3.26 - 3.81: 10761 3.81 - 4.35: 12971 4.35 - 4.90: 22172 Nonbonded interactions: 53341 Sorted by model distance: nonbonded pdb=" OH TYR C 82 " pdb=" O3 FK5 C 201 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR A 219 " pdb=" O LEU A 395 " model vdw 2.212 3.040 nonbonded pdb=" O GLY B 105 " pdb=" OH TYR B 112 " model vdw 2.221 3.040 nonbonded pdb=" O SER C 39 " pdb=" OG SER C 39 " model vdw 2.260 3.040 nonbonded pdb=" O PHE B 238 " pdb=" NH1 ARG B 291 " model vdw 2.279 3.120 ... (remaining 53336 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.440 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.540 Find NCS groups from input model: 0.070 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 0.104 7178 Z= 0.388 Angle : 0.864 11.588 9743 Z= 0.513 Chirality : 0.059 0.661 1102 Planarity : 0.004 0.037 1232 Dihedral : 14.029 79.529 2582 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.41 % Allowed : 1.22 % Favored : 98.37 % Cbeta Deviations : 0.36 % 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 (0.29), residues: 877 helix: 0.22 (0.25), residues: 435 sheet: -2.37 (0.60), residues: 66 loop : -1.43 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 59 HIS 0.014 0.001 HIS B 280 PHE 0.025 0.002 PHE A 223 TYR 0.018 0.002 TYR A 449 ARG 0.004 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 193 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7186 (t80) REVERT: B 315 ASN cc_start: 0.8603 (t0) cc_final: 0.8339 (t0) REVERT: C 11 ASP cc_start: 0.8247 (t70) cc_final: 0.7864 (t70) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.1890 time to fit residues: 31.6435 Evaluate side-chains 99 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.0070 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 435 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.172934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.146999 restraints weight = 8449.293| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.65 r_work: 0.3651 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7178 Z= 0.207 Angle : 0.621 11.436 9743 Z= 0.313 Chirality : 0.042 0.172 1102 Planarity : 0.004 0.031 1232 Dihedral : 5.700 40.932 1003 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.04 % Allowed : 8.70 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.30), residues: 877 helix: 0.68 (0.26), residues: 439 sheet: -2.32 (0.56), residues: 75 loop : -1.28 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 231 HIS 0.005 0.001 HIS B 280 PHE 0.014 0.001 PHE A 242 TYR 0.017 0.001 TYR B 261 ARG 0.003 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.778 Fit side-chains REVERT: A 72 ILE cc_start: 0.8313 (mm) cc_final: 0.8059 (mm) REVERT: A 193 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7461 (t80) REVERT: A 259 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7302 (mpp) REVERT: B 315 ASN cc_start: 0.8847 (t0) cc_final: 0.8583 (t0) REVERT: C 5 GLU cc_start: 0.7393 (pm20) cc_final: 0.7177 (pm20) REVERT: C 11 ASP cc_start: 0.8219 (t70) cc_final: 0.7769 (t70) outliers start: 15 outliers final: 9 residues processed: 115 average time/residue: 0.1630 time to fit residues: 26.4264 Evaluate side-chains 104 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain C residue 8 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 0.0050 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 269 GLN B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.169687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142568 restraints weight = 8770.049| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.91 r_work: 0.3496 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7178 Z= 0.179 Angle : 0.587 11.209 9743 Z= 0.294 Chirality : 0.040 0.131 1102 Planarity : 0.003 0.029 1232 Dihedral : 5.457 37.735 1003 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.45 % Allowed : 11.96 % Favored : 85.60 % 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: -0.36 (0.30), residues: 877 helix: 0.90 (0.26), residues: 441 sheet: -2.27 (0.56), residues: 75 loop : -1.15 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 173 HIS 0.002 0.000 HIS B 198 PHE 0.010 0.001 PHE B 333 TYR 0.013 0.001 TYR B 261 ARG 0.003 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.735 Fit side-chains REVERT: A 72 ILE cc_start: 0.8255 (mm) cc_final: 0.8001 (mm) REVERT: A 99 TRP cc_start: 0.6702 (OUTLIER) cc_final: 0.5694 (t60) REVERT: A 193 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7459 (t80) REVERT: A 379 LYS cc_start: 0.8340 (pptt) cc_final: 0.8137 (pptt) REVERT: B 102 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: B 298 PHE cc_start: 0.7300 (m-80) cc_final: 0.6737 (t80) REVERT: C 11 ASP cc_start: 0.8245 (t70) cc_final: 0.7850 (t70) outliers start: 18 outliers final: 12 residues processed: 114 average time/residue: 0.1579 time to fit residues: 25.6990 Evaluate side-chains 107 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 77 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141921 restraints weight = 8765.403| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.90 r_work: 0.3495 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7178 Z= 0.204 Angle : 0.606 13.333 9743 Z= 0.298 Chirality : 0.041 0.129 1102 Planarity : 0.003 0.030 1232 Dihedral : 5.415 38.967 1003 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.26 % Allowed : 14.13 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.30), residues: 877 helix: 1.03 (0.26), residues: 439 sheet: -2.23 (0.56), residues: 75 loop : -1.16 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 173 HIS 0.002 0.001 HIS B 26 PHE 0.013 0.001 PHE B 333 TYR 0.011 0.001 TYR B 174 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.697 Fit side-chains REVERT: A 72 ILE cc_start: 0.8324 (mm) cc_final: 0.8074 (mm) REVERT: A 193 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7540 (t80) REVERT: A 435 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7561 (t0) REVERT: B 98 MET cc_start: 0.7763 (mmm) cc_final: 0.7534 (mmm) REVERT: B 102 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: C 5 GLU cc_start: 0.7315 (pm20) cc_final: 0.6921 (pm20) REVERT: C 11 ASP cc_start: 0.8260 (t70) cc_final: 0.7822 (t70) outliers start: 24 outliers final: 17 residues processed: 116 average time/residue: 0.1478 time to fit residues: 24.7499 Evaluate side-chains 119 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.0060 chunk 28 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.169341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141897 restraints weight = 8660.356| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.91 r_work: 0.3493 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7178 Z= 0.199 Angle : 0.612 13.796 9743 Z= 0.298 Chirality : 0.040 0.128 1102 Planarity : 0.003 0.029 1232 Dihedral : 5.335 39.775 1003 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.80 % Allowed : 13.99 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.30), residues: 877 helix: 1.07 (0.26), residues: 439 sheet: -2.14 (0.56), residues: 75 loop : -1.13 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 173 HIS 0.002 0.000 HIS B 280 PHE 0.013 0.001 PHE B 333 TYR 0.012 0.001 TYR B 174 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.851 Fit side-chains REVERT: A 72 ILE cc_start: 0.8247 (mm) cc_final: 0.7983 (mm) REVERT: A 193 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7590 (t80) REVERT: B 50 MET cc_start: 0.7610 (ttm) cc_final: 0.7350 (mmm) REVERT: B 102 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: B 151 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: B 298 PHE cc_start: 0.7204 (m-80) cc_final: 0.6666 (t80) REVERT: C 11 ASP cc_start: 0.8243 (t70) cc_final: 0.7851 (t70) outliers start: 28 outliers final: 18 residues processed: 120 average time/residue: 0.1732 time to fit residues: 30.0107 Evaluate side-chains 117 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.170920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143969 restraints weight = 8676.606| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.72 r_work: 0.3467 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7178 Z= 0.208 Angle : 0.601 13.544 9743 Z= 0.296 Chirality : 0.041 0.126 1102 Planarity : 0.003 0.029 1232 Dihedral : 5.314 40.262 1003 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.12 % Allowed : 15.49 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.30), residues: 877 helix: 1.06 (0.26), residues: 439 sheet: -2.02 (0.57), residues: 75 loop : -1.10 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 173 HIS 0.002 0.001 HIS B 280 PHE 0.015 0.001 PHE B 333 TYR 0.012 0.001 TYR B 174 ARG 0.003 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.787 Fit side-chains REVERT: A 72 ILE cc_start: 0.8241 (mm) cc_final: 0.7974 (mm) REVERT: A 193 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7656 (t80) REVERT: A 435 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.7687 (t0) REVERT: B 50 MET cc_start: 0.7807 (ttm) cc_final: 0.7564 (mmm) REVERT: B 70 ILE cc_start: 0.8063 (tp) cc_final: 0.7762 (tt) REVERT: B 102 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: B 151 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: B 298 PHE cc_start: 0.7327 (m-80) cc_final: 0.6892 (t80) REVERT: C 5 GLU cc_start: 0.7282 (pm20) cc_final: 0.6902 (pm20) REVERT: C 11 ASP cc_start: 0.8226 (t70) cc_final: 0.7786 (t70) outliers start: 23 outliers final: 17 residues processed: 115 average time/residue: 0.1493 time to fit residues: 24.7463 Evaluate side-chains 116 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.169953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141774 restraints weight = 8657.514| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.94 r_work: 0.3442 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7178 Z= 0.229 Angle : 0.628 13.562 9743 Z= 0.306 Chirality : 0.041 0.125 1102 Planarity : 0.003 0.029 1232 Dihedral : 5.364 40.196 1003 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.85 % Allowed : 16.85 % Favored : 80.30 % 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: -0.23 (0.30), residues: 877 helix: 0.99 (0.26), residues: 440 sheet: -1.98 (0.57), residues: 75 loop : -1.14 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 173 HIS 0.002 0.001 HIS B 26 PHE 0.018 0.001 PHE B 333 TYR 0.013 0.001 TYR B 174 ARG 0.003 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.727 Fit side-chains REVERT: A 72 ILE cc_start: 0.8257 (mm) cc_final: 0.7993 (mm) REVERT: A 193 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7682 (t80) REVERT: A 259 MET cc_start: 0.7745 (tmm) cc_final: 0.7298 (mmt) REVERT: B 70 ILE cc_start: 0.8109 (tp) cc_final: 0.7781 (tt) REVERT: B 102 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: B 151 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: B 298 PHE cc_start: 0.7336 (m-80) cc_final: 0.6880 (t80) REVERT: C 5 GLU cc_start: 0.7404 (pm20) cc_final: 0.7016 (pm20) REVERT: C 11 ASP cc_start: 0.8305 (t70) cc_final: 0.7874 (t70) outliers start: 21 outliers final: 18 residues processed: 111 average time/residue: 0.1552 time to fit residues: 24.5935 Evaluate side-chains 118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 0.0870 chunk 4 optimal weight: 2.9990 chunk 72 optimal weight: 0.0170 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 34 optimal weight: 0.0470 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.175840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.147703 restraints weight = 8683.001| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.73 r_work: 0.3560 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7178 Z= 0.142 Angle : 0.577 14.029 9743 Z= 0.281 Chirality : 0.039 0.122 1102 Planarity : 0.003 0.027 1232 Dihedral : 4.897 38.385 1003 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.90 % Allowed : 17.93 % Favored : 80.16 % 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: 0.01 (0.31), residues: 877 helix: 1.27 (0.26), residues: 440 sheet: -1.95 (0.58), residues: 75 loop : -1.10 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 173 HIS 0.003 0.000 HIS B 280 PHE 0.011 0.001 PHE A 444 TYR 0.012 0.001 TYR B 174 ARG 0.003 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.802 Fit side-chains REVERT: A 193 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7559 (t80) REVERT: A 259 MET cc_start: 0.7513 (tmm) cc_final: 0.7111 (mmt) REVERT: B 70 ILE cc_start: 0.8077 (tp) cc_final: 0.7771 (tt) REVERT: B 98 MET cc_start: 0.7711 (mmm) cc_final: 0.7124 (mmm) REVERT: B 102 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: B 151 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: C 5 GLU cc_start: 0.7349 (pm20) cc_final: 0.6932 (pm20) REVERT: C 11 ASP cc_start: 0.8229 (t70) cc_final: 0.7785 (t70) outliers start: 14 outliers final: 10 residues processed: 123 average time/residue: 0.1650 time to fit residues: 28.8625 Evaluate side-chains 112 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 0.0570 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.170119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140806 restraints weight = 8737.818| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.06 r_work: 0.3400 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7178 Z= 0.217 Angle : 0.627 13.284 9743 Z= 0.308 Chirality : 0.041 0.123 1102 Planarity : 0.003 0.029 1232 Dihedral : 5.203 38.045 1003 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.90 % Allowed : 19.43 % Favored : 78.67 % 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: -0.01 (0.30), residues: 877 helix: 1.25 (0.26), residues: 440 sheet: -1.95 (0.63), residues: 65 loop : -1.17 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 173 HIS 0.002 0.001 HIS B 48 PHE 0.016 0.001 PHE B 333 TYR 0.020 0.001 TYR B 287 ARG 0.002 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.696 Fit side-chains REVERT: A 193 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7709 (t80) REVERT: A 230 LEU cc_start: 0.7885 (tp) cc_final: 0.7587 (tt) REVERT: A 259 MET cc_start: 0.7658 (tmm) cc_final: 0.7071 (mmt) REVERT: B 70 ILE cc_start: 0.8056 (tp) cc_final: 0.7698 (tp) REVERT: B 102 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: B 151 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: B 298 PHE cc_start: 0.7352 (m-80) cc_final: 0.6925 (t80) REVERT: C 5 GLU cc_start: 0.7482 (pm20) cc_final: 0.7084 (pm20) REVERT: C 11 ASP cc_start: 0.8297 (t70) cc_final: 0.7833 (t70) outliers start: 14 outliers final: 11 residues processed: 109 average time/residue: 0.1573 time to fit residues: 24.3253 Evaluate side-chains 111 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.0270 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142916 restraints weight = 8922.276| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.73 r_work: 0.3434 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7178 Z= 0.229 Angle : 0.649 13.390 9743 Z= 0.315 Chirality : 0.041 0.122 1102 Planarity : 0.003 0.029 1232 Dihedral : 5.293 38.088 1003 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.45 % Allowed : 19.29 % Favored : 78.26 % 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: -0.09 (0.30), residues: 877 helix: 1.20 (0.26), residues: 440 sheet: -1.94 (0.64), residues: 65 loop : -1.24 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 173 HIS 0.003 0.001 HIS B 48 PHE 0.017 0.001 PHE B 333 TYR 0.020 0.001 TYR B 287 ARG 0.002 0.000 ARG B 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.797 Fit side-chains REVERT: A 193 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7604 (t80) REVERT: A 230 LEU cc_start: 0.7991 (tp) cc_final: 0.7703 (tt) REVERT: A 259 MET cc_start: 0.7596 (tmm) cc_final: 0.7053 (mmt) REVERT: B 70 ILE cc_start: 0.8071 (tp) cc_final: 0.7725 (tp) REVERT: B 102 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: B 151 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: B 298 PHE cc_start: 0.7294 (m-80) cc_final: 0.6839 (t80) REVERT: C 5 GLU cc_start: 0.7499 (pm20) cc_final: 0.7123 (pm20) REVERT: C 11 ASP cc_start: 0.8320 (t70) cc_final: 0.7891 (t70) outliers start: 18 outliers final: 15 residues processed: 108 average time/residue: 0.1651 time to fit residues: 25.6670 Evaluate side-chains 113 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 70 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.170656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141435 restraints weight = 8711.507| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.05 r_work: 0.3427 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7178 Z= 0.194 Angle : 0.625 13.145 9743 Z= 0.303 Chirality : 0.040 0.122 1102 Planarity : 0.003 0.028 1232 Dihedral : 5.161 37.394 1003 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.58 % Allowed : 19.43 % Favored : 77.99 % 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: -0.03 (0.30), residues: 877 helix: 1.26 (0.26), residues: 440 sheet: -1.96 (0.63), residues: 65 loop : -1.21 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 173 HIS 0.002 0.000 HIS B 48 PHE 0.014 0.001 PHE B 333 TYR 0.020 0.001 TYR B 287 ARG 0.003 0.000 ARG B 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3798.26 seconds wall clock time: 65 minutes 59.28 seconds (3959.28 seconds total)