Starting phenix.real_space_refine on Wed Feb 12 01:49:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chu_45602/02_2025/9chu_45602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chu_45602/02_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_45602/02_2025/9chu_45602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chu_45602/02_2025/9chu_45602.map" model { file = "/net/cci-nas-00/data/ceres_data/9chu_45602/02_2025/9chu_45602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chu_45602/02_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-5592/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: 5.06, per 1000 atoms: 0.72 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: 1.62 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.69 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: 1.82 Time building geometry restraints manager: 1.84 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.240 Find NCS groups from input model: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.080 ------------------------------------------------------------------------------- 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 : 0.768 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: 0.1964 time to fit residues: 32.9084 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 : 0.729 ------------------------------------------------------------------------------- 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 = 0.146998 restraints weight = 8449.288| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.65 r_work: 0.3650 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.828 Fit side-chains REVERT: A 72 ILE cc_start: 0.8310 (mm) cc_final: 0.8058 (mm) REVERT: A 193 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7465 (t80) REVERT: A 259 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7312 (mpp) REVERT: B 315 ASN cc_start: 0.8844 (t0) cc_final: 0.8582 (t0) REVERT: C 5 GLU cc_start: 0.7396 (pm20) cc_final: 0.7173 (pm20) REVERT: C 11 ASP cc_start: 0.8220 (t70) cc_final: 0.7772 (t70) outliers start: 15 outliers final: 9 residues processed: 115 average time/residue: 0.1670 time to fit residues: 27.1063 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 : 0.721 ------------------------------------------------------------------------------- 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: 0.6980 chunk 59 optimal weight: 0.0870 chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 0.0050 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.4372 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.168477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.140956 restraints weight = 8821.632| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.95 r_work: 0.3507 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1492 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= 0.184 Angle : 0.590 11.212 9743 Z= 0.295 Chirality : 0.040 0.131 1102 Planarity : 0.003 0.029 1232 Dihedral : 5.472 37.768 1003 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.45 % Allowed : 11.82 % Favored : 85.73 % 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: -0.37 (0.30), residues: 877 helix: 0.90 (0.26), residues: 440 sheet: -2.27 (0.56), residues: 75 loop : -1.16 (0.36), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 173 HIS 0.002 0.000 HIS B 280 PHE 0.011 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 : 0.613 Fit side-chains REVERT: A 72 ILE cc_start: 0.8261 (mm) cc_final: 0.8007 (mm) REVERT: A 99 TRP cc_start: 0.6699 (OUTLIER) cc_final: 0.5692 (t60) REVERT: A 166 PHE cc_start: 0.6718 (m-10) cc_final: 0.6515 (m-10) REVERT: A 193 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7466 (t80) REVERT: A 379 LYS cc_start: 0.8339 (pptt) cc_final: 0.8111 (pptt) REVERT: B 98 MET cc_start: 0.7680 (mmm) cc_final: 0.7473 (mmm) REVERT: B 102 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: B 298 PHE cc_start: 0.7305 (m-80) cc_final: 0.6740 (t80) REVERT: C 11 ASP cc_start: 0.8249 (t70) cc_final: 0.7846 (t70) outliers start: 18 outliers final: 12 residues processed: 114 average time/residue: 0.1596 time to fit residues: 25.7997 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 : 0.802 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.169145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141605 restraints weight = 8767.111| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.92 r_work: 0.3497 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7178 Z= 0.224 Angle : 0.613 13.557 9743 Z= 0.303 Chirality : 0.041 0.129 1102 Planarity : 0.003 0.030 1232 Dihedral : 5.490 39.222 1003 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.53 % Allowed : 14.13 % Favored : 82.34 % 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: -0.33 (0.30), residues: 877 helix: 0.98 (0.26), residues: 439 sheet: -2.24 (0.56), residues: 75 loop : -1.21 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 173 HIS 0.002 0.001 HIS B 26 PHE 0.015 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 124 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.804 Fit side-chains REVERT: A 72 ILE cc_start: 0.8262 (mm) cc_final: 0.8002 (mm) REVERT: A 99 TRP cc_start: 0.6721 (OUTLIER) cc_final: 0.5739 (t60) REVERT: A 193 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7473 (t80) REVERT: A 435 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7545 (t0) REVERT: B 98 MET cc_start: 0.7602 (mmm) cc_final: 0.7192 (mmm) REVERT: B 102 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: C 5 GLU cc_start: 0.7171 (pm20) cc_final: 0.6911 (pm20) REVERT: C 11 ASP cc_start: 0.8239 (t70) cc_final: 0.7829 (t70) outliers start: 26 outliers final: 18 residues processed: 116 average time/residue: 0.1625 time to fit residues: 26.9463 Evaluate side-chains 118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR 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 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 6 THR 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: 0.7980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.170007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142554 restraints weight = 8684.329| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.87 r_work: 0.3431 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7178 Z= 0.206 Angle : 0.615 13.631 9743 Z= 0.301 Chirality : 0.041 0.128 1102 Planarity : 0.003 0.030 1232 Dihedral : 5.398 39.755 1003 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.80 % Allowed : 15.35 % Favored : 80.84 % 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: -0.25 (0.30), residues: 877 helix: 1.03 (0.26), residues: 439 sheet: -2.16 (0.56), residues: 75 loop : -1.17 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 173 HIS 0.002 0.000 HIS B 280 PHE 0.014 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 130 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.885 Fit side-chains REVERT: A 72 ILE cc_start: 0.8207 (mm) cc_final: 0.7964 (mm) REVERT: A 193 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7678 (t80) REVERT: A 435 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7650 (t0) REVERT: B 98 MET cc_start: 0.7764 (mmm) cc_final: 0.7554 (mmm) REVERT: B 102 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: B 151 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: B 298 PHE cc_start: 0.7361 (m-80) cc_final: 0.6807 (t80) REVERT: C 11 ASP cc_start: 0.8210 (t70) cc_final: 0.7748 (t70) outliers start: 28 outliers final: 17 residues processed: 123 average time/residue: 0.1572 time to fit residues: 27.5948 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 : 0.742 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 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 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 = 0.3974 r_free = 0.3974 target = 0.168726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142209 restraints weight = 8722.469| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.75 r_work: 0.3387 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7178 Z= 0.253 Angle : 0.629 13.522 9743 Z= 0.310 Chirality : 0.042 0.127 1102 Planarity : 0.003 0.030 1232 Dihedral : 5.498 40.694 1003 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.85 % Allowed : 16.30 % Favored : 80.84 % 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: -0.33 (0.30), residues: 877 helix: 0.92 (0.26), residues: 440 sheet: -2.02 (0.58), residues: 75 loop : -1.20 (0.35), residues: 362 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 0.019 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 120 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.848 Fit side-chains REVERT: A 72 ILE cc_start: 0.8274 (mm) cc_final: 0.7998 (mm) REVERT: A 193 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7688 (t80) REVERT: B 70 ILE cc_start: 0.8121 (tp) cc_final: 0.7808 (tt) REVERT: B 102 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: B 298 PHE cc_start: 0.7333 (m-80) cc_final: 0.6828 (t80) REVERT: C 5 GLU cc_start: 0.7367 (pm20) cc_final: 0.6987 (pm20) REVERT: C 11 ASP cc_start: 0.8270 (t70) cc_final: 0.7826 (t70) outliers start: 21 outliers final: 17 residues processed: 113 average time/residue: 0.1527 time to fit residues: 24.6869 Evaluate side-chains 114 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 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 B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.169866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142755 restraints weight = 8654.940| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.71 r_work: 0.3454 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7178 Z= 0.232 Angle : 0.632 13.336 9743 Z= 0.310 Chirality : 0.041 0.125 1102 Planarity : 0.003 0.030 1232 Dihedral : 5.443 40.739 1003 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.26 % Allowed : 17.12 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.30), residues: 877 helix: 0.91 (0.26), residues: 441 sheet: -1.96 (0.59), residues: 75 loop : -1.24 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 173 HIS 0.002 0.001 HIS B 280 PHE 0.018 0.001 PHE B 333 TYR 0.013 0.001 TYR B 174 ARG 0.002 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 125 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.748 Fit side-chains REVERT: A 72 ILE cc_start: 0.8265 (mm) cc_final: 0.7998 (mm) REVERT: A 193 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7682 (t80) REVERT: A 259 MET cc_start: 0.7684 (tmm) cc_final: 0.7260 (mmt) REVERT: A 435 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7633 (t0) REVERT: B 70 ILE cc_start: 0.8125 (tp) cc_final: 0.7797 (tt) REVERT: B 102 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: B 151 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: B 298 PHE cc_start: 0.7295 (m-80) cc_final: 0.6834 (t80) REVERT: C 5 GLU cc_start: 0.7446 (pm20) cc_final: 0.7076 (pm20) REVERT: C 11 ASP cc_start: 0.8422 (t70) cc_final: 0.7944 (t70) outliers start: 24 outliers final: 19 residues processed: 117 average time/residue: 0.1542 time to fit residues: 25.7120 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 : 0.890 ------------------------------------------------------------------------------- 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 186 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 211 ILE 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: 0.6980 chunk 4 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.169786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142460 restraints weight = 8770.857| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.73 r_work: 0.3525 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7178 Z= 0.228 Angle : 0.646 13.480 9743 Z= 0.314 Chirality : 0.041 0.125 1102 Planarity : 0.003 0.030 1232 Dihedral : 5.425 40.865 1003 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.12 % Allowed : 17.53 % Favored : 79.35 % 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: -0.32 (0.30), residues: 877 helix: 0.96 (0.26), residues: 439 sheet: -2.02 (0.59), residues: 76 loop : -1.24 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 173 HIS 0.002 0.001 HIS B 280 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 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 122 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.825 Fit side-chains REVERT: A 72 ILE cc_start: 0.8336 (mm) cc_final: 0.8051 (mm) REVERT: A 193 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7674 (t80) REVERT: A 259 MET cc_start: 0.7590 (tmm) cc_final: 0.7115 (mmt) REVERT: B 70 ILE cc_start: 0.8152 (tp) cc_final: 0.7832 (tt) REVERT: B 102 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: B 151 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: B 298 PHE cc_start: 0.7325 (m-80) cc_final: 0.6846 (t80) REVERT: C 5 GLU cc_start: 0.7491 (pm20) cc_final: 0.7078 (pm20) REVERT: C 11 ASP cc_start: 0.8466 (t70) cc_final: 0.8111 (t70) outliers start: 23 outliers final: 19 residues processed: 114 average time/residue: 0.1656 time to fit residues: 26.9813 Evaluate side-chains 121 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 211 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.171460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142997 restraints weight = 8740.718| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.90 r_work: 0.3440 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2251 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= 0.175 Angle : 0.605 13.751 9743 Z= 0.295 Chirality : 0.040 0.130 1102 Planarity : 0.003 0.028 1232 Dihedral : 5.183 39.677 1003 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.58 % Allowed : 19.16 % 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: -0.15 (0.30), residues: 877 helix: 1.14 (0.26), residues: 440 sheet: -1.98 (0.59), residues: 76 loop : -1.21 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 173 HIS 0.003 0.000 HIS B 280 PHE 0.012 0.001 PHE B 333 TYR 0.012 0.001 TYR B 174 ARG 0.003 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 125 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.716 Fit side-chains REVERT: A 72 ILE cc_start: 0.8244 (mm) cc_final: 0.7973 (mm) REVERT: A 193 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7617 (t80) REVERT: A 259 MET cc_start: 0.7588 (tmm) cc_final: 0.6984 (mmt) REVERT: B 70 ILE cc_start: 0.8091 (tp) cc_final: 0.7779 (tt) REVERT: B 102 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: B 151 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: B 298 PHE cc_start: 0.7307 (m-80) cc_final: 0.6919 (t80) REVERT: C 5 GLU cc_start: 0.7465 (pm20) cc_final: 0.7076 (pm20) REVERT: C 11 ASP cc_start: 0.8418 (t70) cc_final: 0.8062 (t70) outliers start: 19 outliers final: 16 residues processed: 117 average time/residue: 0.1594 time to fit residues: 26.4447 Evaluate side-chains 118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 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 211 ILE 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 34 optimal weight: 0.0040 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.169562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143300 restraints weight = 8928.437| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.74 r_work: 0.3467 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7178 Z= 0.199 Angle : 0.632 13.348 9743 Z= 0.305 Chirality : 0.041 0.124 1102 Planarity : 0.003 0.029 1232 Dihedral : 5.264 38.957 1003 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.99 % Allowed : 19.16 % Favored : 77.85 % 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: -0.12 (0.30), residues: 877 helix: 1.17 (0.26), residues: 440 sheet: -2.07 (0.64), residues: 66 loop : -1.20 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 173 HIS 0.002 0.000 HIS B 48 PHE 0.015 0.001 PHE B 333 TYR 0.022 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 118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.838 Fit side-chains REVERT: A 193 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7578 (t80) REVERT: A 259 MET cc_start: 0.7572 (tmm) cc_final: 0.7014 (mmt) REVERT: A 435 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.7602 (t0) REVERT: B 70 ILE cc_start: 0.8121 (tp) cc_final: 0.7788 (tt) REVERT: B 102 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: B 151 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: B 246 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.4805 (m-70) REVERT: B 298 PHE cc_start: 0.7247 (m-80) cc_final: 0.6879 (t80) REVERT: C 5 GLU cc_start: 0.7487 (pm20) cc_final: 0.7102 (pm20) REVERT: C 11 ASP cc_start: 0.8441 (t70) cc_final: 0.8090 (t70) outliers start: 22 outliers final: 17 residues processed: 110 average time/residue: 0.1602 time to fit residues: 25.2199 Evaluate side-chains 118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 435 ASN Chi-restraints excluded: chain B residue 42 VAL 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 211 ILE Chi-restraints excluded: chain B residue 246 HIS 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: 0.8980 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 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 ** 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 = 0.3996 r_free = 0.3996 target = 0.171025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142781 restraints weight = 8750.458| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.95 r_work: 0.3449 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.003 0.026 7178 Z= 0.210 Angle : 0.631 13.030 9743 Z= 0.306 Chirality : 0.041 0.122 1102 Planarity : 0.003 0.030 1232 Dihedral : 5.267 38.814 1003 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.99 % Allowed : 19.16 % Favored : 77.85 % 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: 1.18 (0.26), residues: 439 sheet: -2.06 (0.64), residues: 66 loop : -1.17 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 173 HIS 0.002 0.001 HIS B 48 PHE 0.016 0.001 PHE B 333 TYR 0.021 0.001 TYR B 287 ARG 0.002 0.000 ARG B 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3673.72 seconds wall clock time: 65 minutes 59.43 seconds (3959.43 seconds total)