Starting phenix.real_space_refine on Fri Aug 22 16:43:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w8n_21575/08_2025/6w8n_21575.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w8n_21575/08_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_21575/08_2025/6w8n_21575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w8n_21575/08_2025/6w8n_21575.map" model { file = "/net/cci-nas-00/data/ceres_data/6w8n_21575/08_2025/6w8n_21575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w8n_21575/08_2025/6w8n_21575.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'HIS:plan': 2, 'ARG:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 1.88, per 1000 atoms: 0.31 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: 0.40 Conformation dependent library (CDL) restraints added in 310.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.21 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: 0.93 Time building geometry restraints manager: 0.52 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.240 Find NCS groups from input model: 0.100 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.250 ------------------------------------------------------------------------------- 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 6306 Z= 0.283 Angle : 0.774 9.512 8607 Z= 0.423 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 : 12.66 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 35 TYR 0.016 0.002 TYR A 359 PHE 0.015 0.002 PHE A 459 TRP 0.011 0.002 TRP B 394 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00658 ( 6304) covalent geometry : angle 0.77257 ( 8603) SS BOND : bond 0.01239 ( 2) SS BOND : angle 2.44299 ( 4) hydrogen bonds : bond 0.11368 ( 418) hydrogen bonds : angle 4.64802 ( 1242) *********************** 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 : 0.173 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: 0.0644 time to fit residues: 13.0322 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 : 0.216 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.0570 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 71 GLN A 191 GLN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS A 452 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.151440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119310 restraints weight = 7374.202| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.96 r_work: 0.3146 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6306 Z= 0.136 Angle : 0.660 10.151 8607 Z= 0.325 Chirality : 0.043 0.200 1075 Planarity : 0.004 0.042 1044 Dihedral : 11.068 89.883 923 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 6.49 % Allowed : 25.19 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.29), residues: 788 helix: -0.23 (0.20), residues: 616 sheet: None (None), residues: 0 loop : -2.58 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 260 TYR 0.017 0.002 TYR A 313 PHE 0.021 0.001 PHE A 459 TRP 0.012 0.002 TRP B 324 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6304) covalent geometry : angle 0.65882 ( 8603) SS BOND : bond 0.00627 ( 2) SS BOND : angle 1.80360 ( 4) hydrogen bonds : bond 0.04001 ( 418) hydrogen bonds : angle 4.11750 ( 1242) *********************** 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 128 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 85 time to evaluate : 0.213 Fit side-chains REVERT: A 101 VAL cc_start: 0.8318 (p) cc_final: 0.8054 (p) REVERT: A 104 LYS cc_start: 0.8512 (mptm) cc_final: 0.8114 (mptt) REVERT: A 280 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8280 (mt) REVERT: A 336 LYS cc_start: 0.8587 (tttp) cc_final: 0.8360 (tttm) REVERT: A 394 TRP cc_start: 0.8956 (OUTLIER) cc_final: 0.8502 (t-100) REVERT: A 448 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.5717 (t80) REVERT: A 460 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5830 (tt) REVERT: B 104 LYS cc_start: 0.8506 (mptm) cc_final: 0.8116 (mptt) REVERT: B 335 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8032 (ptp-170) REVERT: B 336 LYS cc_start: 0.8618 (tttp) cc_final: 0.8361 (tttm) REVERT: B 394 TRP cc_start: 0.8955 (OUTLIER) cc_final: 0.8481 (t-100) outliers start: 43 outliers final: 23 residues processed: 124 average time/residue: 0.0536 time to fit residues: 9.0812 Evaluate side-chains 108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 375 ARG 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 189 VAL 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 13 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 0.0050 chunk 74 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 72 optimal weight: 0.0870 overall best weight: 0.3572 ------------------------------------------------------------------------------- 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** B 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.155634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123411 restraints weight = 7287.818| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.97 r_work: 0.3197 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6306 Z= 0.119 Angle : 0.599 9.151 8607 Z= 0.294 Chirality : 0.041 0.219 1075 Planarity : 0.004 0.040 1044 Dihedral : 8.713 61.279 885 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.33 % Allowed : 27.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.30), residues: 788 helix: 0.45 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.47 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.014 0.001 TYR A 313 PHE 0.012 0.001 PHE A 459 TRP 0.012 0.001 TRP B 324 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6304) covalent geometry : angle 0.59814 ( 8603) SS BOND : bond 0.00961 ( 2) SS BOND : angle 1.88574 ( 4) hydrogen bonds : bond 0.03587 ( 418) hydrogen bonds : angle 3.98369 ( 1242) *********************** 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 129 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 0.240 Fit side-chains REVERT: A 101 VAL cc_start: 0.8261 (p) cc_final: 0.8007 (p) REVERT: A 104 LYS cc_start: 0.8363 (mptm) cc_final: 0.8024 (mptt) REVERT: A 147 VAL cc_start: 0.8309 (p) cc_final: 0.8058 (t) REVERT: A 336 LYS cc_start: 0.8457 (tttp) cc_final: 0.8206 (tttm) REVERT: A 394 TRP cc_start: 0.8915 (OUTLIER) cc_final: 0.8471 (t-100) REVERT: A 448 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.5782 (t80) REVERT: A 460 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5980 (tt) REVERT: B 35 ARG cc_start: 0.8352 (ttt180) cc_final: 0.8099 (ttt-90) REVERT: B 104 LYS cc_start: 0.8364 (mptm) cc_final: 0.8027 (mptt) REVERT: B 147 VAL cc_start: 0.8280 (p) cc_final: 0.8056 (t) REVERT: B 335 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7826 (ptp-170) REVERT: B 336 LYS cc_start: 0.8507 (tttp) cc_final: 0.8222 (tttm) REVERT: B 394 TRP cc_start: 0.8907 (OUTLIER) cc_final: 0.8441 (t-100) REVERT: B 448 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.5981 (t80) outliers start: 42 outliers final: 21 residues processed: 120 average time/residue: 0.0588 time to fit residues: 9.6366 Evaluate side-chains 105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 375 ARG 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 196 CYS Chi-restraints excluded: chain B residue 335 ARG 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 Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 17 optimal weight: 0.0470 chunk 73 optimal weight: 0.0170 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- 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 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.164303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132812 restraints weight = 7194.006| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.92 r_work: 0.3235 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6306 Z= 0.121 Angle : 0.595 9.161 8607 Z= 0.293 Chirality : 0.040 0.198 1075 Planarity : 0.004 0.039 1044 Dihedral : 7.524 59.498 872 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 7.69 % Allowed : 25.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.30), residues: 788 helix: 0.74 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.43 (0.43), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.013 0.001 TYR B 313 PHE 0.012 0.001 PHE A 459 TRP 0.010 0.001 TRP B 324 HIS 0.004 0.000 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6304) covalent geometry : angle 0.59201 ( 8603) SS BOND : bond 0.00704 ( 2) SS BOND : angle 2.95118 ( 4) hydrogen bonds : bond 0.03451 ( 418) hydrogen bonds : angle 3.98941 ( 1242) *********************** 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 133 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 82 time to evaluate : 0.219 Fit side-chains REVERT: A 101 VAL cc_start: 0.8202 (p) cc_final: 0.7963 (p) REVERT: A 104 LYS cc_start: 0.8331 (mptm) cc_final: 0.7976 (mptt) REVERT: A 117 MET cc_start: 0.8767 (mmp) cc_final: 0.8500 (mmp) REVERT: A 147 VAL cc_start: 0.8231 (p) cc_final: 0.8029 (t) REVERT: A 280 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8183 (mt) REVERT: A 336 LYS cc_start: 0.8428 (tttp) cc_final: 0.8212 (tttm) REVERT: A 359 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.6867 (t80) REVERT: A 394 TRP cc_start: 0.8924 (OUTLIER) cc_final: 0.8381 (t-100) REVERT: A 448 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.5939 (t80) REVERT: A 460 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5890 (tt) REVERT: B 104 LYS cc_start: 0.8294 (mptm) cc_final: 0.7956 (mptt) REVERT: B 147 VAL cc_start: 0.8218 (p) cc_final: 0.8009 (t) REVERT: B 336 LYS cc_start: 0.8498 (tttp) cc_final: 0.8211 (tttm) REVERT: B 359 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.6929 (t80) REVERT: B 394 TRP cc_start: 0.8893 (OUTLIER) cc_final: 0.8331 (t-100) REVERT: B 448 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.5740 (t80) outliers start: 51 outliers final: 28 residues processed: 124 average time/residue: 0.0616 time to fit residues: 10.3860 Evaluate side-chains 112 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 105 THR 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 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 375 ARG 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 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 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 448 PHE Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 459 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** B 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122628 restraints weight = 7451.964| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.99 r_work: 0.3169 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6306 Z= 0.141 Angle : 0.602 9.058 8607 Z= 0.295 Chirality : 0.041 0.208 1075 Planarity : 0.004 0.057 1044 Dihedral : 7.478 59.982 869 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.25 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 : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.30), residues: 788 helix: 0.83 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.34 (0.43), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.012 0.002 TYR B 313 PHE 0.024 0.001 PHE B 459 TRP 0.009 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6304) covalent geometry : angle 0.59699 ( 8603) SS BOND : bond 0.01337 ( 2) SS BOND : angle 3.65371 ( 4) hydrogen bonds : bond 0.03655 ( 418) hydrogen bonds : angle 3.93407 ( 1242) *********************** 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 130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 82 time to evaluate : 0.236 Fit side-chains REVERT: A 101 VAL cc_start: 0.8229 (p) cc_final: 0.7985 (p) REVERT: A 104 LYS cc_start: 0.8313 (mptm) cc_final: 0.7930 (mptt) REVERT: A 117 MET cc_start: 0.8788 (mmp) cc_final: 0.8508 (mmp) REVERT: A 147 VAL cc_start: 0.8265 (p) cc_final: 0.8059 (t) REVERT: A 214 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7217 (mtt) REVERT: A 280 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8213 (mt) REVERT: A 336 LYS cc_start: 0.8449 (tttp) cc_final: 0.8233 (tttm) REVERT: A 394 TRP cc_start: 0.8937 (OUTLIER) cc_final: 0.8431 (t-100) REVERT: A 448 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6058 (t80) REVERT: B 104 LYS cc_start: 0.8291 (mptm) cc_final: 0.7924 (mptt) REVERT: B 335 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7887 (ptp-170) REVERT: B 336 LYS cc_start: 0.8523 (tttp) cc_final: 0.8250 (tttm) REVERT: B 394 TRP cc_start: 0.8931 (OUTLIER) cc_final: 0.8404 (t-100) REVERT: B 448 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.5750 (t80) REVERT: B 451 MET cc_start: 0.7121 (tmm) cc_final: 0.6906 (tmm) outliers start: 48 outliers final: 27 residues processed: 118 average time/residue: 0.0653 time to fit residues: 10.4005 Evaluate side-chains 112 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 105 THR 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 214 MET 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 375 ARG 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 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 196 CYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 ARG 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 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 24 optimal weight: 0.0000 chunk 9 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.3342 ------------------------------------------------------------------------------- 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** B 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.155101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122678 restraints weight = 7269.406| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.98 r_work: 0.3203 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6306 Z= 0.116 Angle : 0.597 9.149 8607 Z= 0.293 Chirality : 0.040 0.227 1075 Planarity : 0.004 0.054 1044 Dihedral : 7.354 59.972 869 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 7.39 % Allowed : 26.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.30), residues: 788 helix: 1.01 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.35 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.014 0.001 TYR B 313 PHE 0.020 0.001 PHE B 459 TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6304) covalent geometry : angle 0.59138 ( 8603) SS BOND : bond 0.01316 ( 2) SS BOND : angle 3.71759 ( 4) hydrogen bonds : bond 0.03536 ( 418) hydrogen bonds : angle 3.97281 ( 1242) *********************** 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 127 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 78 time to evaluate : 0.162 Fit side-chains REVERT: A 104 LYS cc_start: 0.8276 (mptm) cc_final: 0.7911 (mptt) REVERT: A 147 VAL cc_start: 0.8204 (p) cc_final: 0.7996 (t) REVERT: A 280 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8181 (mt) REVERT: A 336 LYS cc_start: 0.8393 (tttp) cc_final: 0.8184 (tttm) REVERT: A 359 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.6870 (t80) REVERT: A 394 TRP cc_start: 0.8933 (OUTLIER) cc_final: 0.8397 (t-100) REVERT: A 448 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.5977 (t80) REVERT: B 104 LYS cc_start: 0.8246 (mptm) cc_final: 0.7894 (mptt) REVERT: B 335 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7753 (ptp-170) REVERT: B 336 LYS cc_start: 0.8484 (tttp) cc_final: 0.8210 (tttm) REVERT: B 359 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.6979 (t80) REVERT: B 394 TRP cc_start: 0.8929 (OUTLIER) cc_final: 0.8397 (t-100) REVERT: B 448 PHE cc_start: 0.6785 (OUTLIER) cc_final: 0.5538 (t80) outliers start: 49 outliers final: 29 residues processed: 118 average time/residue: 0.0620 time to fit residues: 9.8445 Evaluate side-chains 114 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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 375 ARG 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 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 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 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 408 SER Chi-restraints excluded: chain B residue 415 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** B 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.156073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123639 restraints weight = 7241.639| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.98 r_work: 0.3180 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6306 Z= 0.123 Angle : 0.606 9.067 8607 Z= 0.291 Chirality : 0.040 0.234 1075 Planarity : 0.004 0.050 1044 Dihedral : 7.275 59.379 869 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 6.79 % Allowed : 27.45 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.30), residues: 788 helix: 1.02 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.32 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.013 0.001 TYR B 313 PHE 0.016 0.001 PHE B 459 TRP 0.009 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6304) covalent geometry : angle 0.60345 ( 8603) SS BOND : bond 0.00961 ( 2) SS BOND : angle 2.39611 ( 4) hydrogen bonds : bond 0.03523 ( 418) hydrogen bonds : angle 3.96087 ( 1242) *********************** 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 125 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 0.205 Fit side-chains REVERT: A 104 LYS cc_start: 0.8251 (mptm) cc_final: 0.7855 (mptt) REVERT: A 280 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8138 (mt) REVERT: A 336 LYS cc_start: 0.8382 (tttp) cc_final: 0.8149 (tttm) REVERT: A 359 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.6812 (t80) REVERT: A 394 TRP cc_start: 0.8916 (OUTLIER) cc_final: 0.8365 (t-100) REVERT: A 448 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6009 (t80) REVERT: B 104 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7820 (mptt) REVERT: B 335 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7744 (ptp-170) REVERT: B 336 LYS cc_start: 0.8492 (tttp) cc_final: 0.8198 (tttm) REVERT: B 359 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.6924 (t80) REVERT: B 394 TRP cc_start: 0.8891 (OUTLIER) cc_final: 0.8309 (t-100) REVERT: B 448 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.5886 (t80) outliers start: 45 outliers final: 30 residues processed: 116 average time/residue: 0.0658 time to fit residues: 10.3233 Evaluate side-chains 116 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 77 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 375 ARG 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 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 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 448 PHE Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 57 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 74 optimal weight: 0.0370 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122958 restraints weight = 7351.548| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.98 r_work: 0.3167 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6306 Z= 0.128 Angle : 0.619 9.057 8607 Z= 0.301 Chirality : 0.040 0.236 1075 Planarity : 0.004 0.049 1044 Dihedral : 7.232 59.389 869 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.64 % Allowed : 27.60 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.30), residues: 788 helix: 1.11 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.26 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.013 0.002 TYR B 313 PHE 0.015 0.001 PHE B 459 TRP 0.008 0.001 TRP B 324 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6304) covalent geometry : angle 0.60597 ( 8603) SS BOND : bond 0.01107 ( 2) SS BOND : angle 6.00313 ( 4) hydrogen bonds : bond 0.03578 ( 418) hydrogen bonds : angle 3.96435 ( 1242) *********************** 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 126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 0.156 Fit side-chains REVERT: A 104 LYS cc_start: 0.8227 (mptm) cc_final: 0.7834 (mptt) REVERT: A 280 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8153 (mt) REVERT: A 336 LYS cc_start: 0.8395 (tttp) cc_final: 0.8161 (tttm) REVERT: A 359 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.6789 (t80) REVERT: A 375 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6558 (mtp85) REVERT: A 394 TRP cc_start: 0.8929 (OUTLIER) cc_final: 0.8373 (t-100) REVERT: A 448 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6098 (t80) REVERT: B 104 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7814 (mptt) REVERT: B 335 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7778 (ptp-170) REVERT: B 336 LYS cc_start: 0.8487 (tttp) cc_final: 0.8211 (tttm) REVERT: B 359 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.6973 (t80) REVERT: B 394 TRP cc_start: 0.8927 (OUTLIER) cc_final: 0.8327 (t-100) REVERT: B 448 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.5828 (t80) outliers start: 44 outliers final: 31 residues processed: 117 average time/residue: 0.0616 time to fit residues: 9.8556 Evaluate side-chains 121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 375 ARG 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 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 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 448 PHE Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 78 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** B 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124048 restraints weight = 7272.953| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.98 r_work: 0.3170 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6306 Z= 0.117 Angle : 0.607 8.999 8607 Z= 0.291 Chirality : 0.040 0.248 1075 Planarity : 0.004 0.048 1044 Dihedral : 7.099 58.983 869 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 6.18 % Allowed : 28.05 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.30), residues: 788 helix: 1.17 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.23 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.013 0.001 TYR B 313 PHE 0.014 0.001 PHE B 459 TRP 0.009 0.001 TRP B 324 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6304) covalent geometry : angle 0.59808 ( 8603) SS BOND : bond 0.00971 ( 2) SS BOND : angle 4.77097 ( 4) hydrogen bonds : bond 0.03465 ( 418) hydrogen bonds : angle 3.90837 ( 1242) *********************** 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 127 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 0.241 Fit side-chains REVERT: A 104 LYS cc_start: 0.8177 (mptm) cc_final: 0.7744 (mptt) REVERT: A 280 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8074 (mt) REVERT: A 336 LYS cc_start: 0.8365 (tttp) cc_final: 0.8126 (tttm) REVERT: A 359 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.6789 (t80) REVERT: A 375 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6529 (mtp85) REVERT: A 394 TRP cc_start: 0.8921 (OUTLIER) cc_final: 0.8332 (t-100) REVERT: A 448 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6233 (t80) REVERT: B 104 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7763 (mppt) REVERT: B 284 ASN cc_start: 0.8424 (t0) cc_final: 0.8077 (t0) REVERT: B 335 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7652 (ptp-170) REVERT: B 336 LYS cc_start: 0.8463 (tttp) cc_final: 0.8191 (tttm) REVERT: B 359 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.6857 (t80) REVERT: B 394 TRP cc_start: 0.8925 (OUTLIER) cc_final: 0.8386 (t-100) REVERT: B 448 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.5824 (t80) outliers start: 41 outliers final: 29 residues processed: 118 average time/residue: 0.0602 time to fit residues: 9.7217 Evaluate side-chains 121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 130 MET 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 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 375 ARG 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 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 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 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 54 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.158555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126576 restraints weight = 7258.765| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.94 r_work: 0.3213 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6306 Z= 0.128 Angle : 0.614 9.059 8607 Z= 0.295 Chirality : 0.041 0.265 1075 Planarity : 0.004 0.048 1044 Dihedral : 6.882 59.215 862 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.49 % Allowed : 27.30 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.30), residues: 788 helix: 1.15 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.13 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.013 0.002 TYR B 313 PHE 0.014 0.001 PHE B 459 TRP 0.008 0.001 TRP B 324 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6304) covalent geometry : angle 0.60726 ( 8603) SS BOND : bond 0.00934 ( 2) SS BOND : angle 4.14262 ( 4) hydrogen bonds : bond 0.03534 ( 418) hydrogen bonds : angle 3.91073 ( 1242) ********************** 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 130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 0.155 Fit side-chains REVERT: A 41 ASP cc_start: 0.8342 (p0) cc_final: 0.8008 (p0) REVERT: A 104 LYS cc_start: 0.8257 (mptm) cc_final: 0.7875 (mptt) REVERT: A 280 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8186 (mt) REVERT: A 336 LYS cc_start: 0.8408 (tttp) cc_final: 0.8177 (tttm) REVERT: A 359 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.6797 (t80) REVERT: A 375 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6692 (mtp85) REVERT: A 394 TRP cc_start: 0.8957 (OUTLIER) cc_final: 0.8441 (t-100) REVERT: A 448 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6335 (t80) REVERT: B 41 ASP cc_start: 0.8313 (p0) cc_final: 0.8003 (p0) REVERT: B 104 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7876 (mptt) REVERT: B 284 ASN cc_start: 0.8477 (t0) cc_final: 0.8164 (t0) REVERT: B 335 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7835 (ptp-170) REVERT: B 336 LYS cc_start: 0.8517 (tttp) cc_final: 0.8256 (tttm) REVERT: B 359 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.6919 (t80) REVERT: B 394 TRP cc_start: 0.8966 (OUTLIER) cc_final: 0.8443 (t-100) REVERT: B 448 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.5910 (t80) outliers start: 43 outliers final: 29 residues processed: 120 average time/residue: 0.0654 time to fit residues: 10.4602 Evaluate side-chains 125 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 130 MET 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 375 ARG 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 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 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 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 38 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 53 optimal weight: 0.0070 chunk 49 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 2 optimal weight: 0.4980 overall best weight: 0.3136 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.164525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.132656 restraints weight = 7167.810| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.93 r_work: 0.3213 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6306 Z= 0.109 Angle : 0.601 9.001 8607 Z= 0.287 Chirality : 0.040 0.259 1075 Planarity : 0.004 0.047 1044 Dihedral : 6.775 58.801 862 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.88 % Allowed : 27.75 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.31), residues: 788 helix: 1.27 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.06 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.013 0.001 TYR B 313 PHE 0.012 0.001 PHE B 459 TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6304) covalent geometry : angle 0.59553 ( 8603) SS BOND : bond 0.00777 ( 2) SS BOND : angle 3.73684 ( 4) hydrogen bonds : bond 0.03349 ( 418) hydrogen bonds : angle 3.86954 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1421.14 seconds wall clock time: 24 minutes 59.88 seconds (1499.88 seconds total)