Starting phenix.real_space_refine on Thu Sep 18 11:09:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o10_49993/09_2025/9o10_49993.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o10_49993/09_2025/9o10_49993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o10_49993/09_2025/9o10_49993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o10_49993/09_2025/9o10_49993.map" model { file = "/net/cci-nas-00/data/ceres_data/9o10_49993/09_2025/9o10_49993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o10_49993/09_2025/9o10_49993.cif" } resolution = 3.0 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= 0.003 sd= 0.021 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: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 5372 2.51 5 N 1332 2.21 5 O 1380 1.98 5 H 8360 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16488 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4122 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4122 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4122 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4122 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 3.30, per 1000 atoms: 0.20 Number of scatterers: 16488 At special positions: 0 Unit cell: (116.472, 119.848, 75.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1380 8.00 N 1332 7.00 C 5372 6.00 H 8360 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 494.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 3 sheets defined 81.6% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 169 through 181 removed outlier: 4.308A pdb=" N LYS B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 185 through 209 Processing helix chain 'B' and resid 226 through 251 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 278 removed outlier: 3.777A pdb=" N ILE B 270 " --> pdb=" O ASP B 266 " (cutoff:3.500A) Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 291 Processing helix chain 'B' and resid 292 through 303 removed outlier: 4.135A pdb=" N ILE B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 Processing helix chain 'B' and resid 314 through 327 Processing helix chain 'B' and resid 327 through 354 Processing helix chain 'B' and resid 363 through 376 removed outlier: 4.354A pdb=" N TRP B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 407 Processing helix chain 'B' and resid 408 through 421 Processing helix chain 'B' and resid 421 through 426 removed outlier: 3.596A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 180 Processing helix chain 'A' and resid 185 through 209 Processing helix chain 'A' and resid 226 through 251 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 288 through 291 Processing helix chain 'A' and resid 292 through 303 removed outlier: 4.275A pdb=" N ILE A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 313 Processing helix chain 'A' and resid 314 through 327 Processing helix chain 'A' and resid 327 through 354 Processing helix chain 'A' and resid 363 through 376 removed outlier: 4.366A pdb=" N TRP A 369 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TRP A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 407 Processing helix chain 'A' and resid 408 through 421 Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.652A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 181 Processing helix chain 'C' and resid 185 through 209 Processing helix chain 'C' and resid 226 through 250 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 281 removed outlier: 3.841A pdb=" N ILE C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 288 through 303 Processing helix chain 'C' and resid 304 through 313 Processing helix chain 'C' and resid 314 through 327 Processing helix chain 'C' and resid 327 through 354 Processing helix chain 'C' and resid 363 through 376 removed outlier: 4.334A pdb=" N TRP C 369 " --> pdb=" O PRO C 365 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 Processing helix chain 'C' and resid 408 through 421 Processing helix chain 'D' and resid 170 through 180 Processing helix chain 'D' and resid 185 through 209 Processing helix chain 'D' and resid 226 through 250 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 281 removed outlier: 3.817A pdb=" N ILE D 270 " --> pdb=" O ASP D 266 " (cutoff:3.500A) Proline residue: D 272 - end of helix removed outlier: 3.926A pdb=" N GLU D 281 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 291 Processing helix chain 'D' and resid 292 through 303 removed outlier: 4.289A pdb=" N ILE D 298 " --> pdb=" O ARG D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 313 Processing helix chain 'D' and resid 314 through 327 Processing helix chain 'D' and resid 327 through 354 Processing helix chain 'D' and resid 363 through 376 removed outlier: 4.365A pdb=" N TRP D 369 " --> pdb=" O PRO D 365 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 407 Processing helix chain 'D' and resid 408 through 421 Processing helix chain 'D' and resid 421 through 427 Processing sheet with id=AA1, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA3, first strand: chain 'D' and resid 216 through 217 615 hydrogen bonds defined for protein. 1746 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: 3.54 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8340 1.03 - 1.23: 25 1.23 - 1.42: 3319 1.42 - 1.62: 4912 1.62 - 1.81: 68 Bond restraints: 16664 Sorted by residual: bond pdb=" N CYS B 167 " pdb=" CA CYS B 167 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N CYS D 167 " pdb=" CA CYS D 167 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N CYS A 167 " pdb=" CA CYS A 167 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N CYS C 167 " pdb=" CA CYS C 167 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N CYS D 167 " pdb=" H CYS D 167 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 ... (remaining 16659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 27962 1.02 - 2.03: 2235 2.03 - 3.05: 46 3.05 - 4.06: 31 4.06 - 5.08: 10 Bond angle restraints: 30284 Sorted by residual: angle pdb=" C THR A 276 " pdb=" N ILE A 277 " pdb=" CA ILE A 277 " ideal model delta sigma weight residual 122.97 120.33 2.64 9.80e-01 1.04e+00 7.28e+00 angle pdb=" C ILE A 277 " pdb=" CA ILE A 277 " pdb=" CB ILE A 277 " ideal model delta sigma weight residual 111.71 110.00 1.71 8.50e-01 1.38e+00 4.03e+00 angle pdb=" C ILE B 409 " pdb=" CA ILE B 409 " pdb=" CB ILE B 409 " ideal model delta sigma weight residual 114.35 112.49 1.86 1.06e+00 8.90e-01 3.08e+00 angle pdb=" C ILE C 409 " pdb=" CA ILE C 409 " pdb=" CB ILE C 409 " ideal model delta sigma weight residual 114.35 112.58 1.77 1.06e+00 8.90e-01 2.78e+00 angle pdb=" CA CYS D 167 " pdb=" N CYS D 167 " pdb=" H CYS D 167 " ideal model delta sigma weight residual 114.00 109.40 4.60 3.00e+00 1.11e-01 2.36e+00 ... (remaining 30279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7424 17.96 - 35.91: 248 35.91 - 53.87: 73 53.87 - 71.82: 40 71.82 - 89.78: 7 Dihedral angle restraints: 7792 sinusoidal: 4156 harmonic: 3636 Sorted by residual: dihedral pdb=" CA LYS A 421 " pdb=" C LYS A 421 " pdb=" N GLU A 422 " pdb=" CA GLU A 422 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LYS B 421 " pdb=" C LYS B 421 " pdb=" N GLU B 422 " pdb=" CA GLU B 422 " ideal model delta harmonic sigma weight residual -180.00 -163.26 -16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA LYS C 421 " pdb=" C LYS C 421 " pdb=" N GLU C 422 " pdb=" CA GLU C 422 " ideal model delta harmonic sigma weight residual -180.00 -164.42 -15.58 0 5.00e+00 4.00e-02 9.71e+00 ... (remaining 7789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 811 0.025 - 0.050: 316 0.050 - 0.075: 157 0.075 - 0.100: 39 0.100 - 0.125: 25 Chirality restraints: 1348 Sorted by residual: chirality pdb=" CA PRO A 410 " pdb=" N PRO A 410 " pdb=" C PRO A 410 " pdb=" CB PRO A 410 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE B 383 " pdb=" N ILE B 383 " pdb=" C ILE B 383 " pdb=" CB ILE B 383 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE A 383 " pdb=" N ILE A 383 " pdb=" C ILE A 383 " pdb=" CB ILE A 383 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 1345 not shown) Planarity restraints: 2368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 409 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO B 410 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 410 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 410 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 409 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO C 410 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 410 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 410 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 418 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C GLU B 418 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU B 418 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE B 419 " 0.009 2.00e-02 2.50e+03 ... (remaining 2365 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 398 2.14 - 2.75: 31517 2.75 - 3.37: 48711 3.37 - 3.98: 58249 3.98 - 4.60: 94343 Nonbonded interactions: 233218 Sorted by model distance: nonbonded pdb=" OE1 GLU D 422 " pdb="HH12 ARG D 425 " model vdw 1.522 2.450 nonbonded pdb=" OG SER A 327 " pdb="HD21 ASN A 415 " model vdw 1.545 2.450 nonbonded pdb=" OG SER B 327 " pdb="HD21 ASN B 415 " model vdw 1.555 2.450 nonbonded pdb=" OG SER D 327 " pdb="HD21 ASN D 415 " model vdw 1.558 2.450 nonbonded pdb=" OG SER C 327 " pdb="HD21 ASN C 415 " model vdw 1.563 2.450 ... (remaining 233213 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.100 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.200 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.003 0.034 8304 Z= 0.154 Angle : 0.462 5.076 11264 Z= 0.258 Chirality : 0.036 0.125 1348 Planarity : 0.004 0.043 1368 Dihedral : 9.235 57.185 2984 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.23 % Allowed : 1.29 % Favored : 98.47 % 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: 2.37 (0.26), residues: 1036 helix: 1.62 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 1.79 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 425 TYR 0.008 0.001 TYR A 273 PHE 0.005 0.001 PHE A 351 TRP 0.009 0.002 TRP D 370 HIS 0.001 0.000 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8304) covalent geometry : angle 0.46240 (11264) hydrogen bonds : bond 0.13183 ( 615) hydrogen bonds : angle 5.18323 ( 1746) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Evaluate side-chains 260 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ARG cc_start: 0.7763 (ttt180) cc_final: 0.7214 (tmm160) outliers start: 2 outliers final: 3 residues processed: 258 average time/residue: 1.2252 time to fit residues: 334.8817 Evaluate side-chains 176 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 409 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.119323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.089018 restraints weight = 38987.050| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.68 r_work: 0.3125 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8304 Z= 0.187 Angle : 0.593 5.227 11264 Z= 0.316 Chirality : 0.036 0.136 1348 Planarity : 0.005 0.048 1368 Dihedral : 4.158 35.734 1118 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.29 % Allowed : 18.19 % Favored : 78.52 % 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: 2.91 (0.27), residues: 1036 helix: 1.88 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 2.45 (0.45), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 425 TYR 0.012 0.001 TYR B 273 PHE 0.011 0.001 PHE D 416 TRP 0.008 0.001 TRP D 370 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8304) covalent geometry : angle 0.59285 (11264) hydrogen bonds : bond 0.04732 ( 615) hydrogen bonds : angle 4.58106 ( 1746) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 LYS cc_start: 0.8556 (mttt) cc_final: 0.8011 (tppt) REVERT: B 274 TYR cc_start: 0.8254 (m-80) cc_final: 0.7998 (m-80) REVERT: B 414 ASN cc_start: 0.8430 (m-40) cc_final: 0.8057 (t0) REVERT: A 172 ARG cc_start: 0.7448 (ttt180) cc_final: 0.6767 (tmm160) REVERT: C 302 MET cc_start: 0.9045 (ttp) cc_final: 0.8632 (ttm) REVERT: C 414 ASN cc_start: 0.8472 (m-40) cc_final: 0.8108 (t0) REVERT: C 418 GLU cc_start: 0.8066 (tt0) cc_final: 0.7861 (tt0) REVERT: D 180 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8483 (tm-30) REVERT: D 215 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7556 (mm-40) REVERT: D 274 TYR cc_start: 0.8178 (m-80) cc_final: 0.7970 (m-80) REVERT: D 421 LYS cc_start: 0.8343 (ptpt) cc_final: 0.7974 (pttt) outliers start: 28 outliers final: 18 residues processed: 202 average time/residue: 1.0899 time to fit residues: 235.1269 Evaluate side-chains 192 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 215 GLN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 426 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 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 = 0.3654 r_free = 0.3654 target = 0.119676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.089827 restraints weight = 39217.558| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.64 r_work: 0.3132 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8304 Z= 0.141 Angle : 0.566 5.577 11264 Z= 0.293 Chirality : 0.036 0.127 1348 Planarity : 0.006 0.060 1368 Dihedral : 3.763 27.628 1114 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.00 % Allowed : 19.37 % Favored : 78.64 % 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: 2.85 (0.27), residues: 1036 helix: 1.93 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 2.10 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 300 TYR 0.013 0.001 TYR A 273 PHE 0.009 0.001 PHE D 416 TRP 0.009 0.001 TRP D 370 HIS 0.001 0.000 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8304) covalent geometry : angle 0.56577 (11264) hydrogen bonds : bond 0.04145 ( 615) hydrogen bonds : angle 4.36275 ( 1746) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 LYS cc_start: 0.8561 (mttt) cc_final: 0.8034 (tppt) REVERT: B 274 TYR cc_start: 0.8330 (m-80) cc_final: 0.8031 (m-80) REVERT: B 414 ASN cc_start: 0.8463 (m-40) cc_final: 0.8114 (t0) REVERT: A 172 ARG cc_start: 0.7439 (ttt180) cc_final: 0.6763 (tmm160) REVERT: A 213 GLU cc_start: 0.9135 (pt0) cc_final: 0.8885 (pm20) REVERT: A 228 GLN cc_start: 0.8617 (mm-40) cc_final: 0.7360 (tt0) REVERT: A 274 TYR cc_start: 0.7673 (m-80) cc_final: 0.7463 (m-80) REVERT: C 215 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7764 (mm-40) REVERT: C 228 GLN cc_start: 0.8652 (mm-40) cc_final: 0.7599 (tt0) REVERT: C 274 TYR cc_start: 0.8076 (m-80) cc_final: 0.7703 (m-80) REVERT: C 302 MET cc_start: 0.9055 (ttp) cc_final: 0.8637 (ttm) REVERT: C 414 ASN cc_start: 0.8483 (m-40) cc_final: 0.8146 (t0) REVERT: C 418 GLU cc_start: 0.8136 (tt0) cc_final: 0.7888 (tt0) REVERT: D 180 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8500 (tm-30) REVERT: D 213 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8814 (mp0) REVERT: D 215 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7281 (mm-40) REVERT: D 225 ASP cc_start: 0.8549 (m-30) cc_final: 0.7967 (m-30) REVERT: D 274 TYR cc_start: 0.8202 (m-80) cc_final: 0.7950 (m-80) REVERT: D 297 GLN cc_start: 0.8947 (mm110) cc_final: 0.8593 (mp10) REVERT: D 414 ASN cc_start: 0.8475 (m-40) cc_final: 0.8127 (t0) REVERT: D 418 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7143 (tm-30) REVERT: D 421 LYS cc_start: 0.8242 (ptpt) cc_final: 0.8014 (ptpt) REVERT: D 422 GLU cc_start: 0.7565 (mp0) cc_final: 0.7284 (mm-30) REVERT: D 425 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7541 (mtm110) outliers start: 17 outliers final: 12 residues processed: 188 average time/residue: 1.1250 time to fit residues: 225.2583 Evaluate side-chains 176 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 426 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 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 = 0.3647 r_free = 0.3647 target = 0.118990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.089112 restraints weight = 39142.797| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.66 r_work: 0.3112 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8304 Z= 0.147 Angle : 0.552 6.233 11264 Z= 0.288 Chirality : 0.035 0.129 1348 Planarity : 0.006 0.061 1368 Dihedral : 3.591 15.580 1112 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.64 % Allowed : 19.72 % Favored : 78.64 % 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: 3.10 (0.27), residues: 1036 helix: 2.10 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 2.23 (0.42), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 425 TYR 0.013 0.001 TYR B 273 PHE 0.009 0.001 PHE C 416 TRP 0.008 0.001 TRP D 370 HIS 0.001 0.000 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8304) covalent geometry : angle 0.55160 (11264) hydrogen bonds : bond 0.03925 ( 615) hydrogen bonds : angle 4.28581 ( 1746) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 GLU cc_start: 0.9118 (pt0) cc_final: 0.8866 (pm20) REVERT: B 253 LYS cc_start: 0.8575 (mttt) cc_final: 0.8036 (tppt) REVERT: B 274 TYR cc_start: 0.8335 (m-80) cc_final: 0.8022 (m-80) REVERT: B 414 ASN cc_start: 0.8473 (m-40) cc_final: 0.8105 (t0) REVERT: B 423 GLN cc_start: 0.7481 (tt0) cc_final: 0.7264 (tt0) REVERT: A 213 GLU cc_start: 0.9123 (pt0) cc_final: 0.8852 (pm20) REVERT: C 215 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7807 (mm-40) REVERT: C 228 GLN cc_start: 0.8668 (mm-40) cc_final: 0.7593 (tt0) REVERT: C 255 TRP cc_start: 0.7925 (t-100) cc_final: 0.7634 (t60) REVERT: C 274 TYR cc_start: 0.8106 (m-80) cc_final: 0.7772 (m-80) REVERT: C 302 MET cc_start: 0.9064 (ttp) cc_final: 0.8670 (ttm) REVERT: C 414 ASN cc_start: 0.8500 (m-40) cc_final: 0.8179 (t0) REVERT: C 418 GLU cc_start: 0.8142 (tt0) cc_final: 0.7891 (tt0) REVERT: D 180 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8526 (tm-30) REVERT: D 213 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8831 (mp0) REVERT: D 215 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7312 (mm-40) REVERT: D 225 ASP cc_start: 0.8512 (m-30) cc_final: 0.8000 (m-30) REVERT: D 274 TYR cc_start: 0.8253 (m-80) cc_final: 0.7946 (m-80) REVERT: D 297 GLN cc_start: 0.8956 (mm110) cc_final: 0.8679 (mm-40) REVERT: D 414 ASN cc_start: 0.8483 (m-40) cc_final: 0.8122 (t0) REVERT: D 421 LYS cc_start: 0.8211 (ptpt) cc_final: 0.7992 (ptpt) REVERT: D 422 GLU cc_start: 0.7611 (mp0) cc_final: 0.7338 (mm-30) outliers start: 14 outliers final: 12 residues processed: 182 average time/residue: 1.0504 time to fit residues: 204.9819 Evaluate side-chains 178 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 426 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.116389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086799 restraints weight = 39675.753| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.65 r_work: 0.3107 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8304 Z= 0.202 Angle : 0.566 5.717 11264 Z= 0.299 Chirality : 0.036 0.132 1348 Planarity : 0.006 0.066 1368 Dihedral : 3.553 15.862 1112 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.23 % Allowed : 19.72 % Favored : 78.05 % 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: 2.97 (0.27), residues: 1036 helix: 2.06 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 1.98 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 293 TYR 0.015 0.001 TYR A 273 PHE 0.009 0.001 PHE D 416 TRP 0.006 0.001 TRP C 370 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8304) covalent geometry : angle 0.56587 (11264) hydrogen bonds : bond 0.03945 ( 615) hydrogen bonds : angle 4.31305 ( 1746) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 GLU cc_start: 0.9127 (pt0) cc_final: 0.8863 (pm20) REVERT: B 253 LYS cc_start: 0.8587 (mttt) cc_final: 0.8019 (tppt) REVERT: B 274 TYR cc_start: 0.8293 (m-80) cc_final: 0.7969 (m-80) REVERT: B 414 ASN cc_start: 0.8454 (m-40) cc_final: 0.8078 (t0) REVERT: A 213 GLU cc_start: 0.9110 (pt0) cc_final: 0.8811 (pm20) REVERT: A 253 LYS cc_start: 0.8740 (mttt) cc_final: 0.8165 (tppt) REVERT: C 213 GLU cc_start: 0.8546 (mp0) cc_final: 0.8316 (mp0) REVERT: C 215 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7733 (mm-40) REVERT: C 228 GLN cc_start: 0.8664 (mm-40) cc_final: 0.7685 (tt0) REVERT: C 274 TYR cc_start: 0.8098 (m-80) cc_final: 0.7696 (m-80) REVERT: C 302 MET cc_start: 0.9032 (ttp) cc_final: 0.8619 (ttm) REVERT: C 414 ASN cc_start: 0.8461 (m-40) cc_final: 0.8116 (t0) REVERT: C 418 GLU cc_start: 0.8199 (tt0) cc_final: 0.7901 (tt0) REVERT: D 180 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8572 (tm-30) REVERT: D 213 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8874 (mp0) REVERT: D 215 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7537 (mm-40) REVERT: D 274 TYR cc_start: 0.8253 (m-80) cc_final: 0.7888 (m-80) REVERT: D 297 GLN cc_start: 0.8952 (mm110) cc_final: 0.8590 (mp10) REVERT: D 414 ASN cc_start: 0.8459 (m-40) cc_final: 0.8089 (t0) REVERT: D 418 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7290 (tm-30) REVERT: D 422 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7169 (mm-30) outliers start: 19 outliers final: 15 residues processed: 181 average time/residue: 1.0530 time to fit residues: 204.2756 Evaluate side-chains 183 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 426 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN C 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.117336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.087541 restraints weight = 39240.408| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.67 r_work: 0.3140 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8304 Z= 0.145 Angle : 0.553 7.594 11264 Z= 0.288 Chirality : 0.035 0.129 1348 Planarity : 0.006 0.089 1368 Dihedral : 3.525 15.144 1112 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.35 % Allowed : 20.07 % Favored : 77.58 % 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: 3.10 (0.27), residues: 1036 helix: 2.17 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 1.99 (0.43), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 425 TYR 0.015 0.001 TYR B 273 PHE 0.008 0.001 PHE C 416 TRP 0.009 0.001 TRP D 370 HIS 0.001 0.000 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8304) covalent geometry : angle 0.55285 (11264) hydrogen bonds : bond 0.03792 ( 615) hydrogen bonds : angle 4.18940 ( 1746) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 GLU cc_start: 0.9111 (pt0) cc_final: 0.8880 (pm20) REVERT: B 228 GLN cc_start: 0.8701 (mm-40) cc_final: 0.7864 (pt0) REVERT: B 253 LYS cc_start: 0.8601 (mttt) cc_final: 0.8052 (tppt) REVERT: B 414 ASN cc_start: 0.8411 (m-40) cc_final: 0.8036 (t0) REVERT: A 179 LEU cc_start: 0.8948 (mp) cc_final: 0.8714 (mp) REVERT: A 213 GLU cc_start: 0.9091 (pt0) cc_final: 0.8815 (pm20) REVERT: A 228 GLN cc_start: 0.8663 (mm-40) cc_final: 0.7472 (tt0) REVERT: A 253 LYS cc_start: 0.8723 (mttt) cc_final: 0.8152 (tppt) REVERT: C 215 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7638 (mm-40) REVERT: C 274 TYR cc_start: 0.8068 (m-80) cc_final: 0.7688 (m-80) REVERT: C 302 MET cc_start: 0.9015 (ttp) cc_final: 0.8602 (ttm) REVERT: C 414 ASN cc_start: 0.8454 (m-40) cc_final: 0.8090 (t0) REVERT: C 418 GLU cc_start: 0.8234 (tt0) cc_final: 0.7946 (tt0) REVERT: D 180 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8568 (tm-30) REVERT: D 213 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8908 (mp0) REVERT: D 215 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7339 (mm-40) REVERT: D 225 ASP cc_start: 0.8501 (m-30) cc_final: 0.7969 (m-30) REVERT: D 253 LYS cc_start: 0.8445 (mttt) cc_final: 0.7892 (tppt) REVERT: D 274 TYR cc_start: 0.8249 (m-80) cc_final: 0.7858 (m-80) REVERT: D 297 GLN cc_start: 0.8951 (mm110) cc_final: 0.8594 (mm-40) REVERT: D 414 ASN cc_start: 0.8452 (m-40) cc_final: 0.8093 (t0) REVERT: D 422 GLU cc_start: 0.7539 (mp0) cc_final: 0.7212 (mm-30) outliers start: 20 outliers final: 14 residues processed: 189 average time/residue: 1.0644 time to fit residues: 215.7787 Evaluate side-chains 181 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 426 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 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 = 0.3625 r_free = 0.3625 target = 0.116872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.087129 restraints weight = 39264.072| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.67 r_work: 0.3134 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8304 Z= 0.162 Angle : 0.554 5.568 11264 Z= 0.291 Chirality : 0.036 0.130 1348 Planarity : 0.006 0.075 1368 Dihedral : 3.456 14.926 1112 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.35 % Allowed : 20.19 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.13 (0.27), residues: 1036 helix: 2.22 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 1.92 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 425 TYR 0.016 0.001 TYR A 273 PHE 0.008 0.001 PHE D 416 TRP 0.007 0.001 TRP C 370 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8304) covalent geometry : angle 0.55386 (11264) hydrogen bonds : bond 0.03773 ( 615) hydrogen bonds : angle 4.17235 ( 1746) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 228 GLN cc_start: 0.8716 (mm-40) cc_final: 0.7777 (tt0) REVERT: B 253 LYS cc_start: 0.8619 (mttt) cc_final: 0.8065 (tppt) REVERT: B 414 ASN cc_start: 0.8454 (m-40) cc_final: 0.8071 (t0) REVERT: A 213 GLU cc_start: 0.9085 (pt0) cc_final: 0.8856 (pm20) REVERT: A 253 LYS cc_start: 0.8761 (mttt) cc_final: 0.8179 (tppt) REVERT: C 215 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7633 (mm-40) REVERT: C 228 GLN cc_start: 0.8676 (mm-40) cc_final: 0.7762 (tt0) REVERT: C 253 LYS cc_start: 0.8488 (mttt) cc_final: 0.7932 (tppt) REVERT: C 274 TYR cc_start: 0.8142 (m-80) cc_final: 0.7757 (m-80) REVERT: C 298 ILE cc_start: 0.8287 (tt) cc_final: 0.7974 (tp) REVERT: C 302 MET cc_start: 0.9056 (ttp) cc_final: 0.8644 (ttm) REVERT: C 414 ASN cc_start: 0.8493 (m-40) cc_final: 0.8141 (t0) REVERT: C 418 GLU cc_start: 0.8282 (tt0) cc_final: 0.7967 (tt0) REVERT: D 215 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7396 (mm-40) REVERT: D 225 ASP cc_start: 0.8480 (m-30) cc_final: 0.7961 (m-30) REVERT: D 253 LYS cc_start: 0.8492 (mttt) cc_final: 0.7931 (tppt) REVERT: D 274 TYR cc_start: 0.8314 (m-80) cc_final: 0.7872 (m-80) REVERT: D 297 GLN cc_start: 0.8959 (mm110) cc_final: 0.8590 (mp10) REVERT: D 414 ASN cc_start: 0.8479 (m-40) cc_final: 0.8117 (t0) REVERT: D 418 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7373 (tm-30) REVERT: D 422 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7140 (mm-30) REVERT: D 426 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7841 (mp10) outliers start: 20 outliers final: 16 residues processed: 187 average time/residue: 1.0877 time to fit residues: 218.7575 Evaluate side-chains 194 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 426 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 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 = 0.3622 r_free = 0.3622 target = 0.116718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.087025 restraints weight = 39416.899| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.67 r_work: 0.3137 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8304 Z= 0.165 Angle : 0.572 5.558 11264 Z= 0.299 Chirality : 0.036 0.129 1348 Planarity : 0.006 0.076 1368 Dihedral : 3.465 16.558 1112 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.23 % Allowed : 21.48 % Favored : 76.29 % 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: 3.18 (0.27), residues: 1036 helix: 2.27 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 1.90 (0.43), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 425 TYR 0.017 0.001 TYR B 273 PHE 0.008 0.001 PHE D 350 TRP 0.007 0.001 TRP D 370 HIS 0.001 0.000 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8304) covalent geometry : angle 0.57159 (11264) hydrogen bonds : bond 0.03728 ( 615) hydrogen bonds : angle 4.15149 ( 1746) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 228 GLN cc_start: 0.8701 (mm-40) cc_final: 0.7772 (tt0) REVERT: B 253 LYS cc_start: 0.8670 (mttt) cc_final: 0.8119 (tppt) REVERT: B 297 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8525 (mp10) REVERT: B 414 ASN cc_start: 0.8420 (m-40) cc_final: 0.8031 (t0) REVERT: A 213 GLU cc_start: 0.9109 (pt0) cc_final: 0.8865 (pm20) REVERT: A 253 LYS cc_start: 0.8741 (mttt) cc_final: 0.8157 (tppt) REVERT: C 215 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7608 (mm-40) REVERT: C 228 GLN cc_start: 0.8685 (mm-40) cc_final: 0.7729 (tt0) REVERT: C 253 LYS cc_start: 0.8466 (mttt) cc_final: 0.7903 (tppt) REVERT: C 274 TYR cc_start: 0.8099 (m-80) cc_final: 0.7646 (m-80) REVERT: C 298 ILE cc_start: 0.8283 (tt) cc_final: 0.7979 (tp) REVERT: C 302 MET cc_start: 0.9045 (ttp) cc_final: 0.8653 (ttm) REVERT: C 414 ASN cc_start: 0.8430 (m-40) cc_final: 0.8096 (t0) REVERT: C 418 GLU cc_start: 0.8288 (tt0) cc_final: 0.7976 (tt0) REVERT: D 215 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7343 (mm-40) REVERT: D 225 ASP cc_start: 0.8468 (m-30) cc_final: 0.7950 (m-30) REVERT: D 253 LYS cc_start: 0.8502 (mttt) cc_final: 0.7944 (tppt) REVERT: D 274 TYR cc_start: 0.8310 (m-80) cc_final: 0.7875 (m-80) REVERT: D 297 GLN cc_start: 0.8935 (mm110) cc_final: 0.8574 (mp10) REVERT: D 414 ASN cc_start: 0.8453 (m-40) cc_final: 0.8092 (t0) REVERT: D 426 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7821 (mp10) outliers start: 19 outliers final: 16 residues processed: 191 average time/residue: 1.0973 time to fit residues: 224.8354 Evaluate side-chains 195 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 426 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087928 restraints weight = 39396.410| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.67 r_work: 0.3165 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8304 Z= 0.140 Angle : 0.571 5.983 11264 Z= 0.297 Chirality : 0.035 0.127 1348 Planarity : 0.006 0.079 1368 Dihedral : 3.507 18.527 1112 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.11 % Allowed : 22.07 % Favored : 75.82 % 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: 3.25 (0.27), residues: 1036 helix: 2.34 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 1.84 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 425 TYR 0.016 0.001 TYR A 273 PHE 0.007 0.001 PHE B 350 TRP 0.009 0.001 TRP C 370 HIS 0.001 0.000 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8304) covalent geometry : angle 0.57110 (11264) hydrogen bonds : bond 0.03632 ( 615) hydrogen bonds : angle 4.10717 ( 1746) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 GLU cc_start: 0.9147 (pt0) cc_final: 0.8869 (pm20) REVERT: B 225 ASP cc_start: 0.8774 (m-30) cc_final: 0.8489 (m-30) REVERT: B 228 GLN cc_start: 0.8688 (mm-40) cc_final: 0.7768 (tt0) REVERT: B 253 LYS cc_start: 0.8592 (mttt) cc_final: 0.8046 (tppt) REVERT: B 297 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8550 (mp10) REVERT: B 302 MET cc_start: 0.8927 (ttp) cc_final: 0.8632 (ttm) REVERT: B 414 ASN cc_start: 0.8393 (m-40) cc_final: 0.8008 (t0) REVERT: A 213 GLU cc_start: 0.9098 (pt0) cc_final: 0.8860 (pm20) REVERT: A 225 ASP cc_start: 0.8875 (m-30) cc_final: 0.8622 (m-30) REVERT: A 228 GLN cc_start: 0.8633 (mm-40) cc_final: 0.7552 (tt0) REVERT: A 253 LYS cc_start: 0.8714 (mttt) cc_final: 0.8137 (tppt) REVERT: C 215 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7611 (mm-40) REVERT: C 228 GLN cc_start: 0.8668 (mm-40) cc_final: 0.7719 (tt0) REVERT: C 253 LYS cc_start: 0.8437 (mttt) cc_final: 0.7883 (tppt) REVERT: C 255 TRP cc_start: 0.8080 (t-100) cc_final: 0.7857 (t60) REVERT: C 274 TYR cc_start: 0.8030 (m-80) cc_final: 0.7571 (m-80) REVERT: C 298 ILE cc_start: 0.8253 (tt) cc_final: 0.7957 (tp) REVERT: C 302 MET cc_start: 0.9007 (ttp) cc_final: 0.8622 (ttm) REVERT: C 355 ASP cc_start: 0.9330 (m-30) cc_final: 0.9124 (m-30) REVERT: C 414 ASN cc_start: 0.8406 (m-40) cc_final: 0.8091 (t0) REVERT: C 418 GLU cc_start: 0.8223 (tt0) cc_final: 0.7907 (tt0) REVERT: D 172 ARG cc_start: 0.7546 (ttt180) cc_final: 0.6945 (tmm160) REVERT: D 215 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7370 (mm-40) REVERT: D 225 ASP cc_start: 0.8427 (m-30) cc_final: 0.7921 (m-30) REVERT: D 228 GLN cc_start: 0.8500 (mp10) cc_final: 0.7834 (tt0) REVERT: D 253 LYS cc_start: 0.8466 (mttt) cc_final: 0.7894 (tppt) REVERT: D 274 TYR cc_start: 0.8258 (m-80) cc_final: 0.7732 (m-80) REVERT: D 297 GLN cc_start: 0.8936 (mm110) cc_final: 0.8581 (mm-40) REVERT: D 414 ASN cc_start: 0.8392 (m-40) cc_final: 0.8041 (t0) REVERT: D 418 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7307 (tm-30) REVERT: D 422 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7116 (mm-30) REVERT: D 426 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7738 (mp10) outliers start: 18 outliers final: 18 residues processed: 191 average time/residue: 0.9831 time to fit residues: 202.5746 Evaluate side-chains 196 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 426 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 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 = 0.3626 r_free = 0.3626 target = 0.116948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.087916 restraints weight = 39530.072| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.62 r_work: 0.3194 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 8304 Z= 0.165 Angle : 0.867 52.502 11264 Z= 0.379 Chirality : 0.076 2.447 1348 Planarity : 0.006 0.080 1368 Dihedral : 3.491 18.684 1112 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.11 % Allowed : 22.65 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.05 (0.26), residues: 1036 helix: 2.24 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.57 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 425 TYR 0.016 0.001 TYR B 273 PHE 0.007 0.001 PHE D 416 TRP 0.007 0.001 TRP C 370 HIS 0.001 0.000 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8304) covalent geometry : angle 0.86724 (11264) hydrogen bonds : bond 0.03634 ( 615) hydrogen bonds : angle 4.14141 ( 1746) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue SER 285 is missing expected H atoms. Skipping. Residue VAL 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 GLU cc_start: 0.9174 (pt0) cc_final: 0.8892 (pm20) REVERT: B 225 ASP cc_start: 0.8742 (m-30) cc_final: 0.8440 (m-30) REVERT: B 228 GLN cc_start: 0.8683 (mm-40) cc_final: 0.7731 (tt0) REVERT: B 253 LYS cc_start: 0.8627 (mttt) cc_final: 0.8090 (tppt) REVERT: B 274 TYR cc_start: 0.8265 (m-80) cc_final: 0.7897 (m-80) REVERT: B 297 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8511 (mp10) REVERT: B 302 MET cc_start: 0.8955 (ttp) cc_final: 0.8679 (ttm) REVERT: B 305 LEU cc_start: 0.7990 (mt) cc_final: 0.7771 (mm) REVERT: B 414 ASN cc_start: 0.8346 (m-40) cc_final: 0.7954 (t0) REVERT: A 213 GLU cc_start: 0.9125 (pt0) cc_final: 0.8900 (pm20) REVERT: A 225 ASP cc_start: 0.8858 (m-30) cc_final: 0.8579 (m-30) REVERT: A 228 GLN cc_start: 0.8623 (mm-40) cc_final: 0.7592 (tt0) REVERT: A 253 LYS cc_start: 0.8682 (mttt) cc_final: 0.8119 (tppt) REVERT: C 215 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7562 (mm-40) REVERT: C 228 GLN cc_start: 0.8658 (mm-40) cc_final: 0.7704 (tt0) REVERT: C 253 LYS cc_start: 0.8413 (mttt) cc_final: 0.7864 (tppt) REVERT: C 255 TRP cc_start: 0.8055 (t-100) cc_final: 0.7825 (t60) REVERT: C 274 TYR cc_start: 0.8006 (m-80) cc_final: 0.7574 (m-80) REVERT: C 298 ILE cc_start: 0.8254 (tt) cc_final: 0.7960 (tp) REVERT: C 302 MET cc_start: 0.8972 (ttp) cc_final: 0.8613 (ttm) REVERT: C 414 ASN cc_start: 0.8363 (m-40) cc_final: 0.8044 (t0) REVERT: C 418 GLU cc_start: 0.8193 (tt0) cc_final: 0.7906 (tt0) REVERT: D 172 ARG cc_start: 0.7524 (ttt180) cc_final: 0.6926 (tmm160) REVERT: D 215 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7415 (mm-40) REVERT: D 225 ASP cc_start: 0.8434 (m-30) cc_final: 0.7944 (m-30) REVERT: D 228 GLN cc_start: 0.8532 (mp10) cc_final: 0.7816 (tt0) REVERT: D 253 LYS cc_start: 0.8431 (mttt) cc_final: 0.7868 (tppt) REVERT: D 274 TYR cc_start: 0.8111 (m-80) cc_final: 0.7723 (m-80) REVERT: D 297 GLN cc_start: 0.8940 (mm110) cc_final: 0.8594 (mm-40) REVERT: D 414 ASN cc_start: 0.8332 (m-40) cc_final: 0.7985 (t0) REVERT: D 426 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7648 (mp10) outliers start: 18 outliers final: 18 residues processed: 190 average time/residue: 0.9862 time to fit residues: 201.3448 Evaluate side-chains 199 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 426 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088128 restraints weight = 39350.620| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.67 r_work: 0.3135 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 8304 Z= 0.160 Angle : 0.761 34.658 11264 Z= 0.347 Chirality : 0.036 0.216 1348 Planarity : 0.006 0.084 1368 Dihedral : 3.419 18.763 1112 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.88 % Allowed : 23.36 % Favored : 74.77 % 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: 3.13 (0.27), residues: 1036 helix: 2.30 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.62 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 293 TYR 0.017 0.001 TYR B 273 PHE 0.007 0.001 PHE D 350 TRP 0.010 0.001 TRP B 176 HIS 0.001 0.000 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8304) covalent geometry : angle 0.76111 (11264) hydrogen bonds : bond 0.03572 ( 615) hydrogen bonds : angle 4.11737 ( 1746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5423.32 seconds wall clock time: 92 minutes 25.27 seconds (5545.27 seconds total)