Starting phenix.real_space_refine on Tue Mar 11 14:30:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w8n_21575/03_2025/6w8n_21575.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w8n_21575/03_2025/6w8n_21575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w8n_21575/03_2025/6w8n_21575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w8n_21575/03_2025/6w8n_21575.map" model { file = "/net/cci-nas-00/data/ceres_data/6w8n_21575/03_2025/6w8n_21575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w8n_21575/03_2025/6w8n_21575.cif" } resolution = 3.2 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= 0.007 sd= 0.093 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 40 5.16 5 C 4084 2.51 5 N 990 2.21 5 O 1046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 6160 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3087 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 383} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3073 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 383} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 4.43, per 1000 atoms: 0.72 Number of scatterers: 6160 At special positions: 0 Unit cell: (94.875, 96.525, 78.375, 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 40 16.00 O 1046 8.00 N 990 7.00 C 4084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.04 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 935.3 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.803A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 66 through 99 Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 136 through 162 removed outlier: 3.990A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.743A pdb=" N SER A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 205 removed outlier: 5.056A pdb=" N GLY A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Proline residue: A 193 - end of helix removed outlier: 3.766A pdb=" N ALA A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 removed outlier: 3.621A pdb=" N VAL A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 257 through 274 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.070A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 306 through 334 removed outlier: 3.681A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 363 removed outlier: 3.626A pdb=" N GLY A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 373 through 396 removed outlier: 3.574A pdb=" N ARG A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.818A pdb=" N TRP A 410 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.973A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 459 through 470 removed outlier: 4.025A pdb=" N LEU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.803A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 66 through 99 Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.628A pdb=" N ALA B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 136 through 162 removed outlier: 3.995A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 205 removed outlier: 5.072A pdb=" N GLY B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix removed outlier: 3.783A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 224 removed outlier: 3.614A pdb=" N VAL B 215 " --> pdb=" O TYR B 211 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 257 through 274 Processing helix chain 'B' and resid 274 through 279 removed outlier: 4.062A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 306 through 334 removed outlier: 3.685A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 363 removed outlier: 3.633A pdb=" N GLY B 342 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 374 through 396 removed outlier: 4.156A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.812A pdb=" N TRP B 410 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 435 removed outlier: 4.976A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 445 through 470 Proline residue: B 456 - end of helix removed outlier: 4.927A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU B 461 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1242 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: 1.74 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1877 1.34 - 1.46: 1221 1.46 - 1.57: 3144 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 6304 Sorted by residual: bond pdb=" CB VAL B 147 " pdb=" CG1 VAL B 147 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.98e+00 bond pdb=" CB VAL A 147 " pdb=" CG1 VAL A 147 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.96e+00 bond pdb=" CB VAL B 268 " pdb=" CG2 VAL B 268 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" CA ILE A 388 " pdb=" C ILE A 388 " ideal model delta sigma weight residual 1.523 1.504 0.019 1.46e-02 4.69e+03 1.74e+00 bond pdb=" CB VAL A 268 " pdb=" CG2 VAL A 268 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 ... (remaining 6299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 8342 1.90 - 3.80: 213 3.80 - 5.71: 39 5.71 - 7.61: 5 7.61 - 9.51: 4 Bond angle restraints: 8603 Sorted by residual: angle pdb=" N SER A 444 " pdb=" CA SER A 444 " pdb=" C SER A 444 " ideal model delta sigma weight residual 112.72 107.66 5.06 1.14e+00 7.69e-01 1.97e+01 angle pdb=" C LEU B 195 " pdb=" N CYS B 196 " pdb=" CA CYS B 196 " ideal model delta sigma weight residual 122.54 117.33 5.21 1.65e+00 3.67e-01 9.98e+00 angle pdb=" C LEU A 195 " pdb=" N CYS A 196 " pdb=" CA CYS A 196 " ideal model delta sigma weight residual 122.54 117.35 5.19 1.65e+00 3.67e-01 9.90e+00 angle pdb=" N LEU B 355 " pdb=" CA LEU B 355 " pdb=" C LEU B 355 " ideal model delta sigma weight residual 113.25 117.24 -3.99 1.30e+00 5.92e-01 9.43e+00 angle pdb=" N LEU A 355 " pdb=" CA LEU A 355 " pdb=" C LEU A 355 " ideal model delta sigma weight residual 113.25 117.22 -3.97 1.30e+00 5.92e-01 9.33e+00 ... (remaining 8598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3208 17.75 - 35.50: 372 35.50 - 53.25: 96 53.25 - 70.99: 21 70.99 - 88.74: 5 Dihedral angle restraints: 3702 sinusoidal: 1350 harmonic: 2352 Sorted by residual: dihedral pdb=" CB CYS A 144 " pdb=" SG CYS A 144 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -155.42 69.42 1 1.00e+01 1.00e-02 6.23e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual -86.00 -155.27 69.27 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CA GLN B 171 " pdb=" C GLN B 171 " pdb=" N ILE B 172 " pdb=" CA ILE B 172 " ideal model delta harmonic sigma weight residual 180.00 -146.04 -33.96 0 5.00e+00 4.00e-02 4.61e+01 ... (remaining 3699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 668 0.038 - 0.076: 297 0.076 - 0.114: 86 0.114 - 0.152: 13 0.152 - 0.190: 11 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CB THR A 58 " pdb=" CA THR A 58 " pdb=" OG1 THR A 58 " pdb=" CG2 THR A 58 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CB THR B 58 " pdb=" CA THR B 58 " pdb=" OG1 THR B 58 " pdb=" CG2 THR B 58 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CB VAL B 101 " pdb=" CA VAL B 101 " pdb=" CG1 VAL B 101 " pdb=" CG2 VAL B 101 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 1072 not shown) Planarity restraints: 1044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 307 " 0.028 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 308 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 298 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C SER A 298 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 299 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 307 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO B 308 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 308 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 308 " -0.022 5.00e-02 4.00e+02 ... (remaining 1041 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1489 2.78 - 3.31: 6153 3.31 - 3.84: 10410 3.84 - 4.37: 12021 4.37 - 4.90: 20530 Nonbonded interactions: 50603 Sorted by model distance: nonbonded pdb=" O GLN A 171 " pdb=" OG SER A 175 " model vdw 2.244 3.040 nonbonded pdb=" O SER B 444 " pdb=" OG SER B 444 " model vdw 2.257 3.040 nonbonded pdb=" O THR A 306 " pdb=" OG1 THR A 306 " model vdw 2.321 3.040 nonbonded pdb=" O THR B 306 " pdb=" OG1 THR B 306 " model vdw 2.327 3.040 nonbonded pdb=" ND2 ASN A 284 " pdb=" OG1 THR A 306 " model vdw 2.338 3.120 ... (remaining 50598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 398 or (resid 3 \ 99 and (name N or name CA or name C or name O or name CB )) or resid 400 through \ 471)) selection = chain 'B' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.990 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.007 0.047 6304 Z= 0.435 Angle : 0.773 9.512 8603 Z= 0.422 Chirality : 0.048 0.190 1075 Planarity : 0.005 0.041 1044 Dihedral : 16.693 88.743 2160 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 8.14 % Allowed : 21.42 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.74 (0.27), residues: 788 helix: -1.31 (0.19), residues: 604 sheet: None (None), residues: 0 loop : -3.02 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.006 0.001 HIS A 328 PHE 0.015 0.002 PHE A 459 TYR 0.016 0.002 TYR A 359 ARG 0.003 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 100 time to evaluate : 0.629 Fit side-chains REVERT: A 101 VAL cc_start: 0.8280 (p) cc_final: 0.8042 (p) REVERT: A 104 LYS cc_start: 0.8459 (mptm) cc_final: 0.8173 (mppt) REVERT: A 336 LYS cc_start: 0.8548 (tttp) cc_final: 0.8263 (tttm) REVERT: A 341 MET cc_start: 0.8079 (mtt) cc_final: 0.7845 (mtt) REVERT: A 390 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: A 448 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.5874 (t80) REVERT: B 104 LYS cc_start: 0.8545 (mptm) cc_final: 0.8218 (mppt) REVERT: B 280 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8317 (mt) REVERT: B 336 LYS cc_start: 0.8578 (tttp) cc_final: 0.8294 (tttm) REVERT: B 341 MET cc_start: 0.8074 (mtt) cc_final: 0.7841 (mtt) outliers start: 54 outliers final: 41 residues processed: 151 average time/residue: 0.1666 time to fit residues: 33.6739 Evaluate side-chains 126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.0570 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 191 GLN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 191 GLN B 284 ASN B 328 HIS B 390 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.152289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120287 restraints weight = 7267.660| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.95 r_work: 0.3143 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6304 Z= 0.187 Angle : 0.655 10.281 8603 Z= 0.322 Chirality : 0.043 0.192 1075 Planarity : 0.004 0.043 1044 Dihedral : 10.982 89.326 923 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.03 % Allowed : 25.94 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.18 (0.29), residues: 788 helix: -0.20 (0.20), residues: 616 sheet: None (None), residues: 0 loop : -2.56 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 324 HIS 0.003 0.001 HIS B 327 PHE 0.018 0.001 PHE A 459 TYR 0.017 0.002 TYR B 313 ARG 0.003 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 0.689 Fit side-chains REVERT: A 101 VAL cc_start: 0.8312 (p) cc_final: 0.8055 (p) REVERT: A 104 LYS cc_start: 0.8480 (mptm) cc_final: 0.8084 (mptt) REVERT: A 280 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8260 (mt) REVERT: A 336 LYS cc_start: 0.8558 (tttp) cc_final: 0.8328 (tttm) REVERT: A 394 TRP cc_start: 0.8941 (OUTLIER) cc_final: 0.8493 (t-100) REVERT: A 448 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.5733 (t80) REVERT: A 460 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5793 (tt) REVERT: B 104 LYS cc_start: 0.8487 (mptm) cc_final: 0.8098 (mptt) REVERT: B 335 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7934 (ptp-170) REVERT: B 336 LYS cc_start: 0.8598 (tttp) cc_final: 0.8336 (tttm) REVERT: B 394 TRP cc_start: 0.8957 (OUTLIER) cc_final: 0.8497 (t-100) outliers start: 40 outliers final: 20 residues processed: 121 average time/residue: 0.1611 time to fit residues: 26.4442 Evaluate side-chains 106 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** 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 = 0.3739 r_free = 0.3739 target = 0.153833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121737 restraints weight = 7358.230| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.95 r_work: 0.3135 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6304 Z= 0.217 Angle : 0.621 9.424 8603 Z= 0.307 Chirality : 0.042 0.223 1075 Planarity : 0.004 0.041 1044 Dihedral : 8.926 63.136 883 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 7.24 % Allowed : 26.55 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.52 (0.29), residues: 788 helix: 0.25 (0.20), residues: 616 sheet: None (None), residues: 0 loop : -2.28 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.004 0.001 HIS A 166 PHE 0.014 0.001 PHE A 459 TYR 0.013 0.002 TYR A 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 86 time to evaluate : 0.618 Fit side-chains REVERT: A 101 VAL cc_start: 0.8290 (p) cc_final: 0.8034 (p) REVERT: A 104 LYS cc_start: 0.8365 (mptm) cc_final: 0.7980 (mptt) REVERT: A 147 VAL cc_start: 0.8296 (p) cc_final: 0.8063 (t) REVERT: A 280 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8254 (mt) REVERT: A 336 LYS cc_start: 0.8529 (tttp) cc_final: 0.8293 (tttm) REVERT: A 394 TRP cc_start: 0.8914 (OUTLIER) cc_final: 0.8456 (t-100) REVERT: A 448 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.5809 (t80) REVERT: A 460 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5933 (tt) REVERT: B 104 LYS cc_start: 0.8357 (mptm) cc_final: 0.7968 (mptt) REVERT: B 147 VAL cc_start: 0.8272 (p) cc_final: 0.8061 (t) REVERT: B 335 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8000 (ptp-170) REVERT: B 336 LYS cc_start: 0.8569 (tttp) cc_final: 0.8289 (tttm) REVERT: B 394 TRP cc_start: 0.8925 (OUTLIER) cc_final: 0.8433 (t-100) REVERT: B 448 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.5988 (t80) outliers start: 48 outliers final: 27 residues processed: 127 average time/residue: 0.1568 time to fit residues: 27.0538 Evaluate side-chains 114 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 448 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 70 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** 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 = 0.3717 r_free = 0.3717 target = 0.152573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120124 restraints weight = 7429.326| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.98 r_work: 0.3136 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6304 Z= 0.197 Angle : 0.602 9.290 8603 Z= 0.296 Chirality : 0.041 0.249 1075 Planarity : 0.004 0.041 1044 Dihedral : 8.439 59.921 880 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 7.09 % Allowed : 26.24 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 788 helix: 0.59 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.09 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.004 0.001 HIS A 166 PHE 0.012 0.001 PHE A 459 TYR 0.014 0.002 TYR B 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 82 time to evaluate : 0.713 Fit side-chains REVERT: A 101 VAL cc_start: 0.8253 (p) cc_final: 0.8017 (p) REVERT: A 104 LYS cc_start: 0.8328 (mptm) cc_final: 0.7937 (mptt) REVERT: A 280 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8203 (mt) REVERT: A 336 LYS cc_start: 0.8474 (tttp) cc_final: 0.8216 (tttm) REVERT: A 394 TRP cc_start: 0.8921 (OUTLIER) cc_final: 0.8437 (t-100) REVERT: A 448 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.5920 (t80) REVERT: A 451 MET cc_start: 0.7024 (tmm) cc_final: 0.6817 (tmm) REVERT: A 460 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5857 (tt) REVERT: B 104 LYS cc_start: 0.8314 (mptm) cc_final: 0.7944 (mptt) REVERT: B 311 LEU cc_start: 0.8483 (mt) cc_final: 0.8203 (mm) REVERT: B 335 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7825 (ptp-170) REVERT: B 336 LYS cc_start: 0.8541 (tttp) cc_final: 0.8264 (tttm) REVERT: B 394 TRP cc_start: 0.8914 (OUTLIER) cc_final: 0.8412 (t-100) REVERT: B 448 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.5919 (t80) outliers start: 47 outliers final: 28 residues processed: 123 average time/residue: 0.1503 time to fit residues: 25.5434 Evaluate side-chains 111 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 448 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.124354 restraints weight = 7237.804| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.92 r_work: 0.3155 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6304 Z= 0.190 Angle : 0.587 9.176 8603 Z= 0.290 Chirality : 0.041 0.215 1075 Planarity : 0.004 0.039 1044 Dihedral : 7.740 59.714 873 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 7.09 % Allowed : 26.09 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.22 (0.30), residues: 788 helix: 0.82 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.26 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.011 0.001 PHE A 459 TYR 0.013 0.002 TYR B 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 0.690 Fit side-chains REVERT: A 101 VAL cc_start: 0.8225 (p) cc_final: 0.7984 (p) REVERT: A 104 LYS cc_start: 0.8261 (mptm) cc_final: 0.7865 (mptt) REVERT: A 280 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8149 (mt) REVERT: A 336 LYS cc_start: 0.8438 (tttp) cc_final: 0.8219 (tttm) REVERT: A 394 TRP cc_start: 0.8911 (OUTLIER) cc_final: 0.8412 (t-100) REVERT: A 448 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.5925 (t80) REVERT: A 451 MET cc_start: 0.6830 (tmm) cc_final: 0.6597 (tmm) REVERT: A 460 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5842 (tt) REVERT: B 104 LYS cc_start: 0.8272 (mptm) cc_final: 0.7895 (mptt) REVERT: B 311 LEU cc_start: 0.8457 (mt) cc_final: 0.8171 (mm) REVERT: B 335 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7834 (ptp-170) REVERT: B 336 LYS cc_start: 0.8495 (tttp) cc_final: 0.8218 (tttm) REVERT: B 394 TRP cc_start: 0.8905 (OUTLIER) cc_final: 0.8395 (t-100) REVERT: B 448 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.5766 (t80) REVERT: B 451 MET cc_start: 0.6928 (tmm) cc_final: 0.6629 (tmm) outliers start: 47 outliers final: 29 residues processed: 117 average time/residue: 0.1543 time to fit residues: 24.8443 Evaluate side-chains 105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 0.0010 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** 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 = 0.3786 r_free = 0.3786 target = 0.157833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125874 restraints weight = 7162.594| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.91 r_work: 0.3185 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6304 Z= 0.175 Angle : 0.602 9.099 8603 Z= 0.294 Chirality : 0.040 0.217 1075 Planarity : 0.004 0.038 1044 Dihedral : 7.602 59.888 871 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 7.69 % Allowed : 25.79 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.31), residues: 788 helix: 1.00 (0.22), residues: 618 sheet: None (None), residues: 0 loop : -2.22 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 324 HIS 0.004 0.001 HIS A 327 PHE 0.031 0.001 PHE B 459 TYR 0.014 0.002 TYR B 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 79 time to evaluate : 0.679 Fit side-chains REVERT: A 101 VAL cc_start: 0.8186 (p) cc_final: 0.7936 (p) REVERT: A 104 LYS cc_start: 0.8266 (mptm) cc_final: 0.7868 (mptt) REVERT: A 280 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8133 (mt) REVERT: A 336 LYS cc_start: 0.8392 (tttp) cc_final: 0.8161 (tttm) REVERT: A 394 TRP cc_start: 0.8889 (OUTLIER) cc_final: 0.8402 (t-100) REVERT: A 448 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.5950 (t80) REVERT: A 451 MET cc_start: 0.6855 (tmm) cc_final: 0.6545 (tmm) REVERT: B 104 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7854 (mptt) REVERT: B 256 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.7774 (tt) REVERT: B 335 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7740 (ptp-170) REVERT: B 336 LYS cc_start: 0.8490 (tttp) cc_final: 0.8212 (tttm) REVERT: B 394 TRP cc_start: 0.8905 (OUTLIER) cc_final: 0.8381 (t-100) REVERT: B 448 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.5387 (t80) REVERT: B 451 MET cc_start: 0.6897 (tmm) cc_final: 0.6560 (tmm) REVERT: B 452 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6523 (mp10) outliers start: 51 outliers final: 28 residues processed: 121 average time/residue: 0.1531 time to fit residues: 25.5029 Evaluate side-chains 113 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.0170 chunk 25 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.153548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121020 restraints weight = 7288.697| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.97 r_work: 0.3158 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6304 Z= 0.187 Angle : 0.604 9.070 8603 Z= 0.291 Chirality : 0.040 0.231 1075 Planarity : 0.004 0.061 1044 Dihedral : 7.309 59.792 869 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 6.79 % Allowed : 27.30 % Favored : 65.91 % 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: 0.47 (0.30), residues: 788 helix: 1.01 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.22 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.021 0.001 PHE B 459 TYR 0.013 0.002 TYR B 313 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 77 time to evaluate : 0.654 Fit side-chains REVERT: A 101 VAL cc_start: 0.8247 (p) cc_final: 0.8005 (p) REVERT: A 104 LYS cc_start: 0.8258 (mptm) cc_final: 0.7877 (mptt) REVERT: A 280 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8130 (mt) REVERT: A 336 LYS cc_start: 0.8403 (tttp) cc_final: 0.8196 (tttm) REVERT: A 359 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.6927 (t80) REVERT: A 394 TRP cc_start: 0.8920 (OUTLIER) cc_final: 0.8409 (t-100) REVERT: A 448 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.5989 (t80) REVERT: A 451 MET cc_start: 0.6812 (tmm) cc_final: 0.6521 (tmm) REVERT: B 104 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7848 (mptt) REVERT: B 256 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.7803 (tt) REVERT: B 335 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7754 (ptp-170) REVERT: B 336 LYS cc_start: 0.8494 (tttp) cc_final: 0.8220 (tttm) REVERT: B 359 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.6999 (t80) REVERT: B 394 TRP cc_start: 0.8925 (OUTLIER) cc_final: 0.8379 (t-100) REVERT: B 448 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.5390 (t80) REVERT: B 451 MET cc_start: 0.6912 (tmm) cc_final: 0.6588 (tmm) REVERT: B 452 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6583 (mp10) outliers start: 45 outliers final: 30 residues processed: 113 average time/residue: 0.1546 time to fit residues: 23.9348 Evaluate side-chains 117 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.0470 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** 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 = 0.3705 r_free = 0.3705 target = 0.152376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.119312 restraints weight = 7263.992| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.03 r_work: 0.3161 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6304 Z= 0.200 Angle : 0.607 9.037 8603 Z= 0.297 Chirality : 0.040 0.232 1075 Planarity : 0.004 0.059 1044 Dihedral : 7.253 59.135 869 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 7.24 % Allowed : 26.70 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.30), residues: 788 helix: 1.05 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.20 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.019 0.001 PHE B 459 TYR 0.013 0.002 TYR B 313 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 79 time to evaluate : 0.633 Fit side-chains REVERT: A 101 VAL cc_start: 0.8250 (p) cc_final: 0.8011 (p) REVERT: A 104 LYS cc_start: 0.8245 (mptm) cc_final: 0.7852 (mptt) REVERT: A 280 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8177 (mt) REVERT: A 336 LYS cc_start: 0.8405 (tttp) cc_final: 0.8203 (tttm) REVERT: A 394 TRP cc_start: 0.8933 (OUTLIER) cc_final: 0.8400 (t-100) REVERT: A 448 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6201 (t80) REVERT: B 104 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7852 (mptt) REVERT: B 256 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7833 (tt) REVERT: B 335 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7842 (ptp-170) REVERT: B 336 LYS cc_start: 0.8509 (tttp) cc_final: 0.8244 (tttm) REVERT: B 394 TRP cc_start: 0.8938 (OUTLIER) cc_final: 0.8384 (t-100) REVERT: B 448 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.5438 (t80) REVERT: B 451 MET cc_start: 0.6971 (tmm) cc_final: 0.6635 (tmm) REVERT: B 452 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6619 (mp10) outliers start: 48 outliers final: 33 residues processed: 118 average time/residue: 0.1546 time to fit residues: 25.0642 Evaluate side-chains 120 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 78 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** 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 = 0.3709 r_free = 0.3709 target = 0.152938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119871 restraints weight = 7344.618| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.04 r_work: 0.3144 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6304 Z= 0.187 Angle : 0.601 9.004 8603 Z= 0.291 Chirality : 0.040 0.249 1075 Planarity : 0.004 0.056 1044 Dihedral : 7.068 59.913 866 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.94 % Allowed : 27.45 % Favored : 65.61 % 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: 0.58 (0.30), residues: 788 helix: 1.12 (0.22), residues: 614 sheet: None (None), residues: 0 loop : -2.25 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 327 PHE 0.016 0.001 PHE B 459 TYR 0.013 0.001 TYR B 313 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 80 time to evaluate : 0.702 Fit side-chains REVERT: A 104 LYS cc_start: 0.8202 (mptm) cc_final: 0.7801 (mptt) REVERT: A 280 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8124 (mt) REVERT: A 336 LYS cc_start: 0.8373 (tttp) cc_final: 0.8163 (tttm) REVERT: A 359 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.6847 (t80) REVERT: A 394 TRP cc_start: 0.8926 (OUTLIER) cc_final: 0.8367 (t-100) REVERT: A 448 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6264 (t80) REVERT: B 104 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7825 (mptt) REVERT: B 256 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.7777 (tt) REVERT: B 284 ASN cc_start: 0.8369 (t0) cc_final: 0.8052 (t0) REVERT: B 335 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7778 (ptp-170) REVERT: B 336 LYS cc_start: 0.8489 (tttp) cc_final: 0.8214 (tttm) REVERT: B 359 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.6967 (t80) REVERT: B 394 TRP cc_start: 0.8920 (OUTLIER) cc_final: 0.8372 (t-100) REVERT: B 448 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.5352 (t80) REVERT: B 451 MET cc_start: 0.6945 (tmm) cc_final: 0.6637 (tmm) REVERT: B 452 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6571 (mp10) outliers start: 46 outliers final: 30 residues processed: 116 average time/residue: 0.1625 time to fit residues: 25.7828 Evaluate side-chains 119 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 390 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.155033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122619 restraints weight = 7336.957| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.98 r_work: 0.3174 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6304 Z= 0.186 Angle : 0.606 8.988 8603 Z= 0.292 Chirality : 0.040 0.261 1075 Planarity : 0.004 0.056 1044 Dihedral : 6.930 59.570 863 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 6.79 % Allowed : 27.75 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.30), residues: 788 helix: 1.14 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.28 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 327 PHE 0.015 0.001 PHE B 459 TYR 0.013 0.002 TYR B 313 ARG 0.002 0.000 ARG B 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 0.683 Fit side-chains REVERT: A 104 LYS cc_start: 0.8240 (mptm) cc_final: 0.7857 (mptt) REVERT: A 280 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8169 (mt) REVERT: A 336 LYS cc_start: 0.8388 (tttp) cc_final: 0.8186 (tttm) REVERT: A 359 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.6874 (t80) REVERT: A 394 TRP cc_start: 0.8940 (OUTLIER) cc_final: 0.8407 (t-100) REVERT: A 448 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6337 (t80) REVERT: B 104 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7858 (mptt) REVERT: B 284 ASN cc_start: 0.8414 (t0) cc_final: 0.8138 (t0) REVERT: B 335 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7877 (ptp-170) REVERT: B 336 LYS cc_start: 0.8520 (tttp) cc_final: 0.8245 (tttm) REVERT: B 359 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.6995 (t80) REVERT: B 394 TRP cc_start: 0.8929 (OUTLIER) cc_final: 0.8369 (t-100) REVERT: B 448 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.5427 (t80) REVERT: B 451 MET cc_start: 0.7003 (tmm) cc_final: 0.6681 (tmm) REVERT: B 452 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6580 (mp10) outliers start: 45 outliers final: 30 residues processed: 114 average time/residue: 0.1658 time to fit residues: 25.5390 Evaluate side-chains 120 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 80 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 0.0980 chunk 34 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** 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 = 0.3735 r_free = 0.3735 target = 0.154771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122421 restraints weight = 7368.504| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.99 r_work: 0.3162 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6304 Z= 0.175 Angle : 0.600 8.989 8603 Z= 0.289 Chirality : 0.040 0.259 1075 Planarity : 0.004 0.055 1044 Dihedral : 6.888 59.688 863 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.64 % Allowed : 27.75 % Favored : 65.61 % 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: 0.65 (0.31), residues: 788 helix: 1.18 (0.22), residues: 614 sheet: None (None), residues: 0 loop : -2.23 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.014 0.001 PHE B 459 TYR 0.013 0.001 TYR B 313 ARG 0.004 0.000 ARG A 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3218.33 seconds wall clock time: 55 minutes 55.46 seconds (3355.46 seconds total)