Starting phenix.real_space_refine on Sat Jun 14 15:11:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o10_49993/06_2025/9o10_49993.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o10_49993/06_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_49993/06_2025/9o10_49993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o10_49993/06_2025/9o10_49993.map" model { file = "/net/cci-nas-00/data/ceres_data/9o10_49993/06_2025/9o10_49993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o10_49993/06_2025/9o10_49993.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ASP:plan': 1} 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: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ASP:plan': 1} 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: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ASP:plan': 1} 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: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 8.07, per 1000 atoms: 0.49 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: 3.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.27 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: 6.40 Time building geometry restraints manager: 4.80 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: 0.03 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: 1.060 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: 0.300 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.610 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 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:26.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (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 TRP 0.009 0.002 TRP D 370 HIS 0.001 0.000 HIS B 231 PHE 0.005 0.001 PHE A 351 TYR 0.008 0.001 TYR A 273 ARG 0.002 0.000 ARG A 425 Details of bonding type rmsd hydrogen bonds : bond 0.13183 ( 615) hydrogen bonds : angle 5.18323 ( 1746) covalent geometry : bond 0.00349 ( 8304) covalent geometry : angle 0.46240 (11264) *********************** 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 : 1.191 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: 2.5601 time to fit residues: 702.8097 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 : 1.255 ------------------------------------------------------------------------------- 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 87 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.117019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.086957 restraints weight = 39507.104| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.66 r_work: 0.3002 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8304 Z= 0.263 Angle : 0.622 5.134 11264 Z= 0.335 Chirality : 0.038 0.137 1348 Planarity : 0.005 0.045 1368 Dihedral : 4.220 36.294 1118 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.40 % Allowed : 17.61 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.27), residues: 1036 helix: 1.78 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 2.27 (0.44), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 370 HIS 0.002 0.001 HIS B 313 PHE 0.012 0.001 PHE D 416 TYR 0.012 0.001 TYR B 273 ARG 0.007 0.001 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.04733 ( 615) hydrogen bonds : angle 4.64698 ( 1746) covalent geometry : bond 0.00572 ( 8304) covalent geometry : angle 0.62222 (11264) *********************** 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 212 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 1.216 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: 0.8691 (mttt) cc_final: 0.8134 (tppt) REVERT: B 274 TYR cc_start: 0.8443 (m-80) cc_final: 0.8155 (m-80) REVERT: B 414 ASN cc_start: 0.8568 (m-40) cc_final: 0.8180 (t0) REVERT: A 172 ARG cc_start: 0.7532 (ttt180) cc_final: 0.6831 (tmm160) REVERT: A 179 LEU cc_start: 0.9116 (mp) cc_final: 0.8866 (mp) REVERT: A 274 TYR cc_start: 0.7911 (m-80) cc_final: 0.7685 (m-80) REVERT: C 213 GLU cc_start: 0.8546 (mp0) cc_final: 0.8312 (mp0) REVERT: C 414 ASN cc_start: 0.8601 (m-40) cc_final: 0.8206 (t0) REVERT: C 418 GLU cc_start: 0.8171 (tt0) cc_final: 0.7966 (tt0) REVERT: D 180 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8515 (tm-30) REVERT: D 215 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7621 (mm-40) REVERT: D 274 TYR cc_start: 0.8348 (m-80) cc_final: 0.7964 (m-80) REVERT: D 421 LYS cc_start: 0.8442 (ptpt) cc_final: 0.7959 (pttt) outliers start: 29 outliers final: 19 residues processed: 204 average time/residue: 2.2393 time to fit residues: 489.7362 Evaluate side-chains 188 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 191 LEU Chi-restraints excluded: chain A residue 196 ILE 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 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 61 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.115860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.085795 restraints weight = 39659.384| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.68 r_work: 0.3073 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8304 Z= 0.238 Angle : 0.599 5.232 11264 Z= 0.317 Chirality : 0.038 0.133 1348 Planarity : 0.006 0.082 1368 Dihedral : 3.777 16.365 1112 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.70 % Allowed : 19.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.27), residues: 1036 helix: 1.81 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 1.99 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 370 HIS 0.001 0.001 HIS B 231 PHE 0.011 0.001 PHE D 416 TYR 0.012 0.001 TYR A 273 ARG 0.011 0.001 ARG D 425 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 615) hydrogen bonds : angle 4.51120 ( 1746) covalent geometry : bond 0.00528 ( 8304) covalent geometry : angle 0.59900 (11264) *********************** 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 200 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.383 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: 0.8661 (mttt) cc_final: 0.8091 (tppt) REVERT: B 274 TYR cc_start: 0.8311 (m-80) cc_final: 0.7979 (m-80) REVERT: B 414 ASN cc_start: 0.8436 (m-40) cc_final: 0.8077 (t0) REVERT: A 172 ARG cc_start: 0.7413 (ttt180) cc_final: 0.6746 (tmm160) REVERT: A 213 GLU cc_start: 0.9158 (pt0) cc_final: 0.8890 (pm20) REVERT: C 213 GLU cc_start: 0.8633 (mp0) cc_final: 0.8417 (mp0) REVERT: C 414 ASN cc_start: 0.8457 (m-40) cc_final: 0.8090 (t0) REVERT: D 215 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7598 (mm-40) REVERT: D 274 TYR cc_start: 0.8192 (m-80) cc_final: 0.7914 (m-80) REVERT: D 418 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7218 (tm-30) REVERT: D 421 LYS cc_start: 0.8248 (ptpt) cc_final: 0.8002 (ptmt) outliers start: 23 outliers final: 15 residues processed: 190 average time/residue: 2.3050 time to fit residues: 469.0968 Evaluate side-chains 188 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 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 251 SER Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 203 THR 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 56 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.117466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087514 restraints weight = 39218.161| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.66 r_work: 0.3091 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3961 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= 0.142 Angle : 0.557 5.652 11264 Z= 0.291 Chirality : 0.036 0.129 1348 Planarity : 0.006 0.059 1368 Dihedral : 3.664 15.145 1112 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.00 % Allowed : 19.13 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.27), residues: 1036 helix: 1.96 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 1.88 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 370 HIS 0.001 0.000 HIS B 231 PHE 0.009 0.001 PHE C 416 TYR 0.014 0.001 TYR B 273 ARG 0.015 0.001 ARG B 425 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 615) hydrogen bonds : angle 4.31497 ( 1746) covalent geometry : bond 0.00312 ( 8304) covalent geometry : angle 0.55730 (11264) *********************** 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 197 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 1.405 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: 0.8586 (mttt) cc_final: 0.8025 (tppt) REVERT: B 274 TYR cc_start: 0.8383 (m-80) cc_final: 0.8016 (m-80) REVERT: B 414 ASN cc_start: 0.8495 (m-40) cc_final: 0.8112 (t0) REVERT: A 213 GLU cc_start: 0.9101 (pt0) cc_final: 0.8841 (pm20) REVERT: A 274 TYR cc_start: 0.7701 (m-80) cc_final: 0.7472 (m-80) REVERT: C 213 GLU cc_start: 0.8688 (mp0) cc_final: 0.8478 (mp0) REVERT: C 228 GLN cc_start: 0.8652 (mm-40) cc_final: 0.7665 (tt0) REVERT: C 255 TRP cc_start: 0.7984 (t-100) cc_final: 0.7675 (t60) REVERT: C 298 ILE cc_start: 0.8300 (tt) cc_final: 0.7975 (tp) REVERT: C 414 ASN cc_start: 0.8525 (m-40) cc_final: 0.8136 (t0) REVERT: C 418 GLU cc_start: 0.8291 (tt0) cc_final: 0.8074 (tt0) REVERT: D 215 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7246 (mm-40) REVERT: D 225 ASP cc_start: 0.8555 (m-30) cc_final: 0.7981 (m-30) REVERT: D 274 TYR cc_start: 0.8299 (m-80) cc_final: 0.7967 (m-80) REVERT: D 414 ASN cc_start: 0.8540 (m-40) cc_final: 0.8123 (t0) REVERT: D 418 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7429 (tm-30) outliers start: 17 outliers final: 15 residues processed: 189 average time/residue: 2.3109 time to fit residues: 467.2642 Evaluate side-chains 183 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 203 THR 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 423 GLN 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 24 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.116182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.086432 restraints weight = 39937.879| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.69 r_work: 0.3107 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8304 Z= 0.167 Angle : 0.559 5.804 11264 Z= 0.294 Chirality : 0.036 0.129 1348 Planarity : 0.006 0.065 1368 Dihedral : 3.577 15.296 1112 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.35 % Allowed : 19.95 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.27), residues: 1036 helix: 2.02 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 1.93 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 370 HIS 0.001 0.000 HIS B 231 PHE 0.009 0.001 PHE D 416 TYR 0.014 0.001 TYR A 273 ARG 0.017 0.001 ARG B 425 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 615) hydrogen bonds : angle 4.28876 ( 1746) covalent geometry : bond 0.00373 ( 8304) covalent geometry : angle 0.55918 (11264) *********************** 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 197 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 GLU cc_start: 0.9125 (pt0) cc_final: 0.8910 (pm20) REVERT: B 228 GLN cc_start: 0.8685 (mm-40) cc_final: 0.7799 (tt0) REVERT: B 253 LYS cc_start: 0.8637 (mttt) cc_final: 0.8079 (tppt) REVERT: B 274 TYR cc_start: 0.8327 (m-80) cc_final: 0.7943 (m-80) REVERT: B 414 ASN cc_start: 0.8443 (m-40) cc_final: 0.8064 (t0) REVERT: A 213 GLU cc_start: 0.9093 (pt0) cc_final: 0.8835 (pm20) REVERT: A 253 LYS cc_start: 0.8750 (mttt) cc_final: 0.8194 (tppt) REVERT: C 213 GLU cc_start: 0.8725 (mp0) cc_final: 0.8489 (mp0) REVERT: C 228 GLN cc_start: 0.8644 (mm-40) cc_final: 0.7636 (tt0) REVERT: C 255 TRP cc_start: 0.7973 (t-100) cc_final: 0.7622 (t60) REVERT: C 298 ILE cc_start: 0.8246 (tt) cc_final: 0.7935 (tp) REVERT: C 414 ASN cc_start: 0.8472 (m-40) cc_final: 0.8092 (t0) REVERT: C 418 GLU cc_start: 0.8233 (tt0) cc_final: 0.8014 (tt0) REVERT: D 213 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8854 (mp0) REVERT: D 215 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7591 (mm-40) REVERT: D 253 LYS cc_start: 0.8468 (mttt) cc_final: 0.7905 (tppt) REVERT: D 274 TYR cc_start: 0.8271 (m-80) cc_final: 0.7886 (m-80) REVERT: D 297 GLN cc_start: 0.8956 (mm110) cc_final: 0.8598 (mp10) REVERT: D 414 ASN cc_start: 0.8492 (m-40) cc_final: 0.8084 (t0) REVERT: D 418 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7379 (tm-30) outliers start: 20 outliers final: 16 residues processed: 187 average time/residue: 2.1777 time to fit residues: 437.6270 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 : 1.450 ------------------------------------------------------------------------------- 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 191 LEU 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 426 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.116696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086792 restraints weight = 39458.263| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.69 r_work: 0.3134 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4255 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= 0.146 Angle : 0.556 6.319 11264 Z= 0.290 Chirality : 0.035 0.129 1348 Planarity : 0.006 0.066 1368 Dihedral : 3.511 15.093 1112 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.23 % Allowed : 20.42 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.27), residues: 1036 helix: 2.10 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 1.94 (0.43), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 370 HIS 0.001 0.000 HIS A 313 PHE 0.008 0.001 PHE D 416 TYR 0.015 0.001 TYR B 273 ARG 0.013 0.001 ARG B 425 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 615) hydrogen bonds : angle 4.20877 ( 1746) covalent geometry : bond 0.00328 ( 8304) covalent geometry : angle 0.55622 (11264) *********************** 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 195 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 GLU cc_start: 0.9107 (pt0) cc_final: 0.8889 (pm20) REVERT: B 228 GLN cc_start: 0.8681 (mm-40) cc_final: 0.7774 (tt0) REVERT: B 253 LYS cc_start: 0.8597 (mttt) cc_final: 0.8026 (tppt) REVERT: B 274 TYR cc_start: 0.8316 (m-80) cc_final: 0.7916 (m-80) REVERT: B 414 ASN cc_start: 0.8412 (m-40) cc_final: 0.8033 (t0) REVERT: A 213 GLU cc_start: 0.9093 (pt0) cc_final: 0.8844 (pm20) REVERT: A 228 GLN cc_start: 0.8639 (mm-40) cc_final: 0.7509 (tt0) REVERT: A 253 LYS cc_start: 0.8750 (mttt) cc_final: 0.8191 (tppt) REVERT: C 213 GLU cc_start: 0.8754 (mp0) cc_final: 0.8396 (mp0) REVERT: C 228 GLN cc_start: 0.8653 (mm-40) cc_final: 0.7630 (tt0) REVERT: C 255 TRP cc_start: 0.7989 (t-100) cc_final: 0.7606 (t60) REVERT: C 298 ILE cc_start: 0.8249 (tt) cc_final: 0.7943 (tp) REVERT: C 414 ASN cc_start: 0.8454 (m-40) cc_final: 0.8078 (t0) REVERT: D 213 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8851 (mp0) REVERT: D 215 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7342 (mm-40) REVERT: D 225 ASP cc_start: 0.8526 (m-30) cc_final: 0.7994 (m-30) REVERT: D 253 LYS cc_start: 0.8445 (mttt) cc_final: 0.7890 (tppt) REVERT: D 274 TYR cc_start: 0.8264 (m-80) cc_final: 0.7857 (m-80) REVERT: D 297 GLN cc_start: 0.8947 (mm110) cc_final: 0.8592 (mp10) REVERT: D 414 ASN cc_start: 0.8468 (m-40) cc_final: 0.8070 (t0) outliers start: 19 outliers final: 14 residues processed: 185 average time/residue: 2.1563 time to fit residues: 429.9963 Evaluate side-chains 182 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 191 LEU 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 426 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.115775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085996 restraints weight = 39573.798| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.68 r_work: 0.3067 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8304 Z= 0.176 Angle : 0.557 5.092 11264 Z= 0.293 Chirality : 0.036 0.131 1348 Planarity : 0.006 0.075 1368 Dihedral : 3.450 15.173 1112 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.11 % Allowed : 21.24 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.27), residues: 1036 helix: 2.17 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 1.96 (0.43), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 370 HIS 0.002 0.001 HIS A 313 PHE 0.008 0.001 PHE D 416 TYR 0.015 0.001 TYR A 273 ARG 0.009 0.001 ARG B 425 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 615) hydrogen bonds : angle 4.20931 ( 1746) covalent geometry : bond 0.00393 ( 8304) covalent geometry : angle 0.55724 (11264) *********************** 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: 18 poor density : 180 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 GLU cc_start: 0.9117 (pt0) cc_final: 0.8901 (pm20) REVERT: B 228 GLN cc_start: 0.8702 (mm-40) cc_final: 0.7784 (tt0) REVERT: B 253 LYS cc_start: 0.8690 (mttt) cc_final: 0.8122 (tppt) REVERT: B 274 TYR cc_start: 0.8403 (m-80) cc_final: 0.7985 (m-80) REVERT: B 414 ASN cc_start: 0.8465 (m-40) cc_final: 0.8069 (t0) REVERT: A 213 GLU cc_start: 0.9096 (pt0) cc_final: 0.8868 (pm20) REVERT: A 228 GLN cc_start: 0.8671 (mm-40) cc_final: 0.7549 (tt0) REVERT: A 253 LYS cc_start: 0.8760 (mttt) cc_final: 0.8190 (tppt) REVERT: C 213 GLU cc_start: 0.8797 (mp0) cc_final: 0.8516 (mp0) REVERT: C 253 LYS cc_start: 0.8540 (mttt) cc_final: 0.7981 (tppt) REVERT: C 298 ILE cc_start: 0.8310 (tt) cc_final: 0.8010 (tp) REVERT: C 302 MET cc_start: 0.9090 (ttp) cc_final: 0.8717 (ttm) REVERT: C 414 ASN cc_start: 0.8494 (m-40) cc_final: 0.8119 (t0) REVERT: D 213 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8845 (mp0) REVERT: D 215 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7409 (mm-40) REVERT: D 225 ASP cc_start: 0.8540 (m-30) cc_final: 0.8026 (m-30) REVERT: D 253 LYS cc_start: 0.8505 (mttt) cc_final: 0.7950 (tppt) REVERT: D 274 TYR cc_start: 0.8341 (m-80) cc_final: 0.7897 (m-80) REVERT: D 297 GLN cc_start: 0.8951 (mm110) cc_final: 0.8592 (mm-40) REVERT: D 414 ASN cc_start: 0.8513 (m-40) cc_final: 0.8100 (t0) REVERT: D 418 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7362 (tm-30) REVERT: D 426 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7745 (mp10) outliers start: 18 outliers final: 15 residues processed: 188 average time/residue: 2.1365 time to fit residues: 432.2183 Evaluate side-chains 190 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 191 LEU 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 426 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.117449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087502 restraints weight = 39353.986| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.71 r_work: 0.3195 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8304 Z= 0.127 Angle : 0.550 5.474 11264 Z= 0.286 Chirality : 0.035 0.130 1348 Planarity : 0.005 0.075 1368 Dihedral : 3.420 16.866 1112 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.76 % Allowed : 21.60 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.27), residues: 1036 helix: 2.27 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 2.02 (0.43), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 370 HIS 0.001 0.001 HIS B 313 PHE 0.007 0.001 PHE C 350 TYR 0.016 0.001 TYR B 273 ARG 0.010 0.001 ARG D 300 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 615) hydrogen bonds : angle 4.09794 ( 1746) covalent geometry : bond 0.00284 ( 8304) covalent geometry : angle 0.55015 (11264) *********************** 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 199 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 GLU cc_start: 0.9099 (pt0) cc_final: 0.8864 (pm20) REVERT: B 225 ASP cc_start: 0.8767 (m-30) cc_final: 0.8528 (m-30) REVERT: B 228 GLN cc_start: 0.8646 (mm-40) cc_final: 0.7691 (tt0) REVERT: B 253 LYS cc_start: 0.8538 (mttt) cc_final: 0.7994 (tppt) REVERT: B 274 TYR cc_start: 0.8204 (m-80) cc_final: 0.7802 (m-80) REVERT: B 297 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8443 (mp10) REVERT: B 414 ASN cc_start: 0.8300 (m-40) cc_final: 0.7926 (t0) REVERT: A 213 GLU cc_start: 0.9106 (pt0) cc_final: 0.8857 (pm20) REVERT: A 225 ASP cc_start: 0.8878 (m-30) cc_final: 0.8625 (m-30) REVERT: A 228 GLN cc_start: 0.8629 (mm-40) cc_final: 0.7512 (tt0) REVERT: A 253 LYS cc_start: 0.8681 (mttt) cc_final: 0.8135 (tppt) REVERT: C 213 GLU cc_start: 0.8792 (mp0) cc_final: 0.8502 (mp0) REVERT: C 228 GLN cc_start: 0.8615 (mm-40) cc_final: 0.7719 (tt0) REVERT: C 253 LYS cc_start: 0.8425 (mttt) cc_final: 0.7883 (tppt) REVERT: C 255 TRP cc_start: 0.8033 (t-100) cc_final: 0.7827 (t60) REVERT: C 298 ILE cc_start: 0.8173 (tt) cc_final: 0.7888 (tp) REVERT: C 302 MET cc_start: 0.8948 (ttp) cc_final: 0.8579 (ttm) REVERT: C 414 ASN cc_start: 0.8304 (m-40) cc_final: 0.7968 (t0) REVERT: D 172 ARG cc_start: 0.7510 (ttt180) cc_final: 0.6903 (tmm160) REVERT: D 213 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8860 (mp0) REVERT: D 215 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7338 (mm-40) REVERT: D 225 ASP cc_start: 0.8450 (m-30) cc_final: 0.7953 (m-30) REVERT: D 228 GLN cc_start: 0.8502 (mp10) cc_final: 0.7871 (tt0) REVERT: D 253 LYS cc_start: 0.8390 (mttt) cc_final: 0.7836 (tppt) REVERT: D 274 TYR cc_start: 0.8162 (m-80) cc_final: 0.7658 (m-80) REVERT: D 297 GLN cc_start: 0.8913 (mm110) cc_final: 0.8558 (mp10) REVERT: D 414 ASN cc_start: 0.8321 (m-40) cc_final: 0.7935 (t0) REVERT: D 426 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7677 (mp10) outliers start: 15 outliers final: 13 residues processed: 189 average time/residue: 1.9724 time to fit residues: 403.2282 Evaluate side-chains 189 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 191 LEU 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 426 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.117695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088213 restraints weight = 39351.101| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.69 r_work: 0.3223 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8304 Z= 0.130 Angle : 0.561 5.744 11264 Z= 0.290 Chirality : 0.036 0.161 1348 Planarity : 0.005 0.078 1368 Dihedral : 3.447 18.079 1112 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.88 % Allowed : 21.71 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.27), residues: 1036 helix: 2.34 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 1.96 (0.43), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 370 HIS 0.001 0.000 HIS A 313 PHE 0.008 0.001 PHE D 350 TYR 0.016 0.001 TYR A 273 ARG 0.010 0.001 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 615) hydrogen bonds : angle 4.07448 ( 1746) covalent geometry : bond 0.00293 ( 8304) covalent geometry : angle 0.56051 (11264) *********************** 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 199 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 GLU cc_start: 0.9097 (pt0) cc_final: 0.8875 (pm20) REVERT: B 225 ASP cc_start: 0.8773 (m-30) cc_final: 0.8529 (m-30) REVERT: B 228 GLN cc_start: 0.8655 (mm-40) cc_final: 0.7724 (tt0) REVERT: B 253 LYS cc_start: 0.8521 (mttt) cc_final: 0.7984 (tppt) REVERT: B 274 TYR cc_start: 0.8130 (m-80) cc_final: 0.7722 (m-80) REVERT: B 297 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8401 (mp10) REVERT: B 302 MET cc_start: 0.8851 (ttp) cc_final: 0.8469 (ttm) REVERT: B 414 ASN cc_start: 0.8254 (m-40) cc_final: 0.7889 (t0) REVERT: A 213 GLU cc_start: 0.9047 (pt0) cc_final: 0.8815 (pm20) REVERT: A 225 ASP cc_start: 0.8863 (m-30) cc_final: 0.8613 (m-30) REVERT: A 228 GLN cc_start: 0.8612 (mm-40) cc_final: 0.7579 (tt0) REVERT: A 253 LYS cc_start: 0.8640 (mttt) cc_final: 0.8090 (tppt) REVERT: A 355 ASP cc_start: 0.9329 (m-30) cc_final: 0.9120 (m-30) REVERT: C 213 GLU cc_start: 0.8804 (mp0) cc_final: 0.8502 (mp0) REVERT: C 228 GLN cc_start: 0.8611 (mm-40) cc_final: 0.7675 (tt0) REVERT: C 253 LYS cc_start: 0.8377 (mttt) cc_final: 0.7838 (tppt) REVERT: C 255 TRP cc_start: 0.8008 (t-100) cc_final: 0.7782 (t60) REVERT: C 298 ILE cc_start: 0.8152 (tt) cc_final: 0.7884 (tp) REVERT: C 302 MET cc_start: 0.8909 (ttp) cc_final: 0.8552 (ttm) REVERT: C 355 ASP cc_start: 0.9319 (m-30) cc_final: 0.9104 (m-30) REVERT: C 414 ASN cc_start: 0.8241 (m-40) cc_final: 0.7921 (t0) REVERT: D 172 ARG cc_start: 0.7465 (ttt180) cc_final: 0.6887 (tmm160) REVERT: D 213 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8863 (mp0) REVERT: D 215 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7362 (mm-40) REVERT: D 225 ASP cc_start: 0.8373 (m-30) cc_final: 0.7971 (m-30) REVERT: D 228 GLN cc_start: 0.8508 (mp10) cc_final: 0.7860 (tt0) REVERT: D 253 LYS cc_start: 0.8371 (mttt) cc_final: 0.7827 (tppt) REVERT: D 274 TYR cc_start: 0.7934 (m-80) cc_final: 0.7578 (m-80) REVERT: D 297 GLN cc_start: 0.8906 (mm110) cc_final: 0.8583 (mm-40) REVERT: D 355 ASP cc_start: 0.9321 (m-30) cc_final: 0.9109 (m-30) REVERT: D 414 ASN cc_start: 0.8276 (m-40) cc_final: 0.7905 (t0) REVERT: D 422 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6774 (mm-30) REVERT: D 426 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7589 (mp10) outliers start: 16 outliers final: 12 residues processed: 188 average time/residue: 2.0096 time to fit residues: 407.9098 Evaluate side-chains 188 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 426 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.116421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086772 restraints weight = 39597.974| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.68 r_work: 0.3178 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8304 Z= 0.171 Angle : 0.586 6.037 11264 Z= 0.306 Chirality : 0.036 0.133 1348 Planarity : 0.006 0.081 1368 Dihedral : 3.435 18.430 1112 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.53 % Allowed : 22.89 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.26), residues: 1036 helix: 2.20 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.60 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 176 HIS 0.001 0.001 HIS A 313 PHE 0.008 0.001 PHE D 416 TYR 0.016 0.001 TYR B 273 ARG 0.017 0.001 ARG D 425 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 615) hydrogen bonds : angle 4.15167 ( 1746) covalent geometry : bond 0.00386 ( 8304) covalent geometry : angle 0.58642 (11264) ********************** 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 188 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 225 ASP cc_start: 0.8791 (m-30) cc_final: 0.8528 (m-30) REVERT: B 228 GLN cc_start: 0.8702 (mm-40) cc_final: 0.7749 (tt0) REVERT: B 253 LYS cc_start: 0.8636 (mttt) cc_final: 0.8090 (tppt) REVERT: B 274 TYR cc_start: 0.8190 (m-80) cc_final: 0.7784 (m-80) REVERT: B 297 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8458 (mp10) REVERT: B 302 MET cc_start: 0.8888 (ttp) cc_final: 0.8507 (ttm) REVERT: B 414 ASN cc_start: 0.8309 (m-40) cc_final: 0.7923 (t0) REVERT: A 213 GLU cc_start: 0.9037 (pt0) cc_final: 0.8778 (pm20) REVERT: A 225 ASP cc_start: 0.8861 (m-30) cc_final: 0.8621 (m-30) REVERT: A 253 LYS cc_start: 0.8670 (mttt) cc_final: 0.8113 (tppt) REVERT: C 213 GLU cc_start: 0.8818 (mp0) cc_final: 0.8536 (mp0) REVERT: C 228 GLN cc_start: 0.8627 (mm-40) cc_final: 0.7720 (tt0) REVERT: C 253 LYS cc_start: 0.8409 (mttt) cc_final: 0.7849 (tppt) REVERT: C 255 TRP cc_start: 0.8040 (t-100) cc_final: 0.7820 (t60) REVERT: C 298 ILE cc_start: 0.8207 (tt) cc_final: 0.7935 (tp) REVERT: C 302 MET cc_start: 0.8951 (ttp) cc_final: 0.8611 (ttm) REVERT: C 355 ASP cc_start: 0.9331 (m-30) cc_final: 0.9129 (m-30) REVERT: C 414 ASN cc_start: 0.8307 (m-40) cc_final: 0.7979 (t0) REVERT: D 172 ARG cc_start: 0.7444 (ttt180) cc_final: 0.6898 (tmm160) REVERT: D 215 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7400 (mm-40) REVERT: D 225 ASP cc_start: 0.8402 (m-30) cc_final: 0.7939 (m-30) REVERT: D 228 GLN cc_start: 0.8528 (mp10) cc_final: 0.7858 (tt0) REVERT: D 253 LYS cc_start: 0.8435 (mttt) cc_final: 0.7890 (tppt) REVERT: D 274 TYR cc_start: 0.8041 (m-80) cc_final: 0.7680 (m-80) REVERT: D 297 GLN cc_start: 0.8916 (mm110) cc_final: 0.8562 (mm-40) REVERT: D 355 ASP cc_start: 0.9325 (m-30) cc_final: 0.9115 (m-30) REVERT: D 414 ASN cc_start: 0.8327 (m-40) cc_final: 0.7940 (t0) REVERT: D 426 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7629 (mp10) outliers start: 13 outliers final: 12 residues processed: 181 average time/residue: 2.0085 time to fit residues: 392.4290 Evaluate side-chains 189 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 426 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 86 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN ** 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 = 0.3646 r_free = 0.3646 target = 0.118310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.089202 restraints weight = 39317.327| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.66 r_work: 0.3212 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8304 Z= 0.128 Angle : 0.586 7.295 11264 Z= 0.301 Chirality : 0.035 0.135 1348 Planarity : 0.006 0.081 1368 Dihedral : 3.397 18.723 1112 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.76 % Allowed : 23.12 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.27), residues: 1036 helix: 2.28 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.66 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 176 HIS 0.001 0.000 HIS A 313 PHE 0.007 0.001 PHE D 350 TYR 0.016 0.001 TYR B 273 ARG 0.012 0.001 ARG D 425 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 615) hydrogen bonds : angle 4.05866 ( 1746) covalent geometry : bond 0.00293 ( 8304) covalent geometry : angle 0.58576 (11264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10932.83 seconds wall clock time: 186 minutes 16.53 seconds (11176.53 seconds total)