Starting phenix.real_space_refine on Tue Mar 3 17:04:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uag_26425/03_2026/7uag_26425.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uag_26425/03_2026/7uag_26425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uag_26425/03_2026/7uag_26425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uag_26425/03_2026/7uag_26425.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uag_26425/03_2026/7uag_26425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uag_26425/03_2026/7uag_26425.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4838 2.51 5 N 1318 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3794 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3794 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLU A 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU A 504 " occ=0.50 residue: pdb=" N GLU B 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B 504 " occ=0.50 Time building chain proxies: 1.82, per 1000 atoms: 0.24 Number of scatterers: 7588 At special positions: 0 Unit cell: (107.07, 125.33, 73.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1392 8.00 N 1318 7.00 C 4838 6.00 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: 0.69 Conformation dependent library (CDL) restraints added in 282.5 milliseconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 42.3% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 41 through 58 removed outlier: 5.272A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix removed outlier: 3.758A pdb=" N ASP A 58 " --> pdb=" O TRP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.958A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 465 removed outlier: 3.617A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.070A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 5.388A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix removed outlier: 3.787A pdb=" N ASP B 58 " --> pdb=" O TRP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 86 through 89 removed outlier: 3.645A pdb=" N LYS B 89 " --> pdb=" O PRO B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.719A pdb=" N ARG B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.727A pdb=" N ILE B 196 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.639A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.249A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 251' Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.663A pdb=" N ASN B 302 " --> pdb=" O GLN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.529A pdb=" N THR B 319 " --> pdb=" O GLY B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.835A pdb=" N ASP B 350 " --> pdb=" O GLU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 454 through 476 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 4.117A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 106 removed outlier: 3.828A pdb=" N VAL A 68 " --> pdb=" O PHE A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 removed outlier: 3.828A pdb=" N VAL A 68 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR A 139 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 35 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 373 removed outlier: 3.571A pdb=" N LYS A 366 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA A 231 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE A 355 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL A 233 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ILE A 480 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 305 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TYR A 482 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN A 307 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 393 Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 407 Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.341A pdb=" N ILE B 33 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TYR B 139 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE B 35 " --> pdb=" O TYR B 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 356 removed outlier: 8.410A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.645A pdb=" N LEU B 305 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR B 482 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN B 307 " --> pdb=" O TYR B 482 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 391 through 393 Processing sheet with id=AB1, first strand: chain 'B' and resid 405 through 407 285 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2296 1.33 - 1.45: 1200 1.45 - 1.57: 4203 1.57 - 1.69: 1 1.69 - 1.81: 66 Bond restraints: 7766 Sorted by residual: bond pdb=" CB PRO A 172 " pdb=" CG PRO A 172 " ideal model delta sigma weight residual 1.506 1.600 -0.094 3.90e-02 6.57e+02 5.76e+00 bond pdb=" C VAL A 68 " pdb=" N GLY A 69 " ideal model delta sigma weight residual 1.328 1.305 0.023 1.13e-02 7.83e+03 4.29e+00 bond pdb=" C VAL B 68 " pdb=" N GLY B 69 " ideal model delta sigma weight residual 1.328 1.305 0.023 1.13e-02 7.83e+03 4.23e+00 bond pdb=" CA GLY B 69 " pdb=" C GLY B 69 " ideal model delta sigma weight residual 1.519 1.495 0.024 1.47e-02 4.63e+03 2.77e+00 bond pdb=" C TYR A 70 " pdb=" O TYR A 70 " ideal model delta sigma weight residual 1.235 1.215 0.021 1.26e-02 6.30e+03 2.65e+00 ... (remaining 7761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 10229 1.77 - 3.53: 227 3.53 - 5.30: 33 5.30 - 7.07: 11 7.07 - 8.84: 2 Bond angle restraints: 10502 Sorted by residual: angle pdb=" CA PRO A 172 " pdb=" N PRO A 172 " pdb=" CD PRO A 172 " ideal model delta sigma weight residual 111.50 105.35 6.15 1.40e+00 5.10e-01 1.93e+01 angle pdb=" N PRO A 172 " pdb=" CD PRO A 172 " pdb=" CG PRO A 172 " ideal model delta sigma weight residual 103.80 98.57 5.23 1.20e+00 6.94e-01 1.90e+01 angle pdb=" C PRO A 276 " pdb=" N ALA A 277 " pdb=" CA ALA A 277 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" N PRO B 172 " pdb=" CD PRO B 172 " pdb=" CG PRO B 172 " ideal model delta sigma weight residual 103.80 99.84 3.96 1.20e+00 6.94e-01 1.09e+01 angle pdb=" CA GLY A 69 " pdb=" C GLY A 69 " pdb=" O GLY A 69 " ideal model delta sigma weight residual 122.76 119.25 3.51 1.12e+00 7.97e-01 9.81e+00 ... (remaining 10497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4262 17.98 - 35.97: 345 35.97 - 53.95: 57 53.95 - 71.93: 7 71.93 - 89.91: 3 Dihedral angle restraints: 4674 sinusoidal: 1944 harmonic: 2730 Sorted by residual: dihedral pdb=" CA MET A 207 " pdb=" C MET A 207 " pdb=" N VAL A 208 " pdb=" CA VAL A 208 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ASN B 218 " pdb=" C ASN B 218 " pdb=" N ARG B 219 " pdb=" CA ARG B 219 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ASN A 218 " pdb=" C ASN A 218 " pdb=" N ARG A 219 " pdb=" CA ARG A 219 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 4671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 593 0.028 - 0.056: 298 0.056 - 0.084: 144 0.084 - 0.111: 64 0.111 - 0.139: 25 Chirality restraints: 1124 Sorted by residual: chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE B 196 " pdb=" N ILE B 196 " pdb=" C ILE B 196 " pdb=" CB ILE B 196 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA THR A 279 " pdb=" N THR A 279 " pdb=" C THR A 279 " pdb=" CB THR A 279 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 1121 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 433 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 434 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 434 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 434 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 352 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 353 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 239 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO A 240 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " -0.031 5.00e-02 4.00e+02 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1594 2.78 - 3.31: 7608 3.31 - 3.84: 12940 3.84 - 4.37: 14984 4.37 - 4.90: 26110 Nonbonded interactions: 63236 Sorted by model distance: nonbonded pdb=" O ILE A 80 " pdb=" OG SER A 84 " model vdw 2.247 3.040 nonbonded pdb=" OE2 GLU A 274 " pdb=" ND2 ASN A 346 " model vdw 2.247 3.120 nonbonded pdb=" OE1 GLN A 209 " pdb=" NZ LYS B 407 " model vdw 2.259 3.120 nonbonded pdb=" OE2 GLU B 274 " pdb=" ND2 ASN B 346 " model vdw 2.261 3.120 nonbonded pdb=" NH2 ARG B 215 " pdb=" O MET B 273 " model vdw 2.278 3.120 ... (remaining 63231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.600 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 : 0.004 0.094 7766 Z= 0.186 Angle : 0.663 8.837 10502 Z= 0.355 Chirality : 0.045 0.139 1124 Planarity : 0.006 0.081 1374 Dihedral : 13.108 89.913 2914 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.45 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.27), residues: 930 helix: 0.02 (0.28), residues: 330 sheet: -2.33 (0.41), residues: 142 loop : -1.13 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 285 TYR 0.013 0.002 TYR B 118 PHE 0.027 0.002 PHE A 173 TRP 0.035 0.002 TRP B 225 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 7766) covalent geometry : angle 0.66257 (10502) hydrogen bonds : bond 0.11986 ( 279) hydrogen bonds : angle 6.49360 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.300 Fit side-chains REVERT: A 70 TYR cc_start: 0.7609 (t80) cc_final: 0.7267 (t80) REVERT: A 111 GLN cc_start: 0.6906 (mm110) cc_final: 0.6329 (mm-40) REVERT: A 137 LEU cc_start: 0.8189 (tt) cc_final: 0.7691 (tt) REVERT: B 70 TYR cc_start: 0.7377 (t80) cc_final: 0.7040 (t80) REVERT: B 111 GLN cc_start: 0.6751 (mm-40) cc_final: 0.6394 (mm-40) REVERT: B 207 MET cc_start: 0.7476 (mmm) cc_final: 0.7265 (mmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0835 time to fit residues: 13.2006 Evaluate side-chains 95 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN B 201 HIS ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.230948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.199132 restraints weight = 9790.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.203283 restraints weight = 6325.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.206050 restraints weight = 4712.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.207583 restraints weight = 3848.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.208996 restraints weight = 3376.511| |-----------------------------------------------------------------------------| r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4473 r_free = 0.4473 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4473 r_free = 0.4473 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7766 Z= 0.155 Angle : 0.612 8.701 10502 Z= 0.317 Chirality : 0.045 0.200 1124 Planarity : 0.005 0.055 1374 Dihedral : 4.617 22.021 1032 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.37 % Allowed : 7.44 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.27), residues: 930 helix: 0.01 (0.28), residues: 330 sheet: -2.34 (0.41), residues: 140 loop : -1.21 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 81 TYR 0.018 0.002 TYR B 484 PHE 0.022 0.002 PHE A 173 TRP 0.018 0.002 TRP B 225 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7766) covalent geometry : angle 0.61172 (10502) hydrogen bonds : bond 0.03737 ( 279) hydrogen bonds : angle 5.45162 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.388 Fit side-chains REVERT: A 70 TYR cc_start: 0.7404 (t80) cc_final: 0.7138 (t80) REVERT: A 95 LYS cc_start: 0.6879 (mmtt) cc_final: 0.6439 (mmtm) REVERT: A 111 GLN cc_start: 0.6765 (mm110) cc_final: 0.6205 (mm-40) REVERT: B 111 GLN cc_start: 0.6744 (mm-40) cc_final: 0.6523 (mm-40) outliers start: 3 outliers final: 2 residues processed: 103 average time/residue: 0.0847 time to fit residues: 12.2911 Evaluate side-chains 95 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 5.9990 chunk 57 optimal weight: 0.0270 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.230797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.198858 restraints weight = 9687.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.202800 restraints weight = 6363.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.205673 restraints weight = 4785.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.207336 restraints weight = 3915.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.208697 restraints weight = 3428.867| |-----------------------------------------------------------------------------| r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4467 r_free = 0.4467 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4467 r_free = 0.4467 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7766 Z= 0.143 Angle : 0.587 8.738 10502 Z= 0.302 Chirality : 0.044 0.164 1124 Planarity : 0.005 0.052 1374 Dihedral : 4.560 23.455 1032 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.73 % Allowed : 10.37 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.27), residues: 930 helix: 0.14 (0.29), residues: 328 sheet: -2.15 (0.41), residues: 138 loop : -1.15 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.020 0.002 TYR B 70 PHE 0.019 0.002 PHE A 173 TRP 0.013 0.002 TRP B 225 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7766) covalent geometry : angle 0.58677 (10502) hydrogen bonds : bond 0.03497 ( 279) hydrogen bonds : angle 5.23361 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.273 Fit side-chains REVERT: A 95 LYS cc_start: 0.6948 (mmtt) cc_final: 0.6523 (mmtm) REVERT: A 111 GLN cc_start: 0.6856 (mm110) cc_final: 0.6571 (mm-40) REVERT: A 244 GLU cc_start: 0.5887 (pm20) cc_final: 0.5367 (pm20) outliers start: 6 outliers final: 3 residues processed: 96 average time/residue: 0.0782 time to fit residues: 10.7032 Evaluate side-chains 95 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 chunk 75 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.227485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.197848 restraints weight = 9523.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.201607 restraints weight = 6286.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.204132 restraints weight = 4708.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.205753 restraints weight = 3858.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.206791 restraints weight = 3389.257| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4472 r_free = 0.4472 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4472 r_free = 0.4472 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7766 Z= 0.142 Angle : 0.573 8.499 10502 Z= 0.293 Chirality : 0.044 0.180 1124 Planarity : 0.005 0.053 1374 Dihedral : 4.531 26.513 1032 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.10 % Allowed : 11.71 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.27), residues: 930 helix: 0.11 (0.29), residues: 332 sheet: -2.29 (0.39), residues: 146 loop : -1.04 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 463 TYR 0.021 0.002 TYR B 70 PHE 0.018 0.002 PHE A 173 TRP 0.011 0.002 TRP B 225 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7766) covalent geometry : angle 0.57280 (10502) hydrogen bonds : bond 0.03346 ( 279) hydrogen bonds : angle 5.16758 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.434 Fit side-chains REVERT: A 95 LYS cc_start: 0.6915 (mmtt) cc_final: 0.6504 (mmtm) REVERT: A 244 GLU cc_start: 0.5764 (pm20) cc_final: 0.5491 (pm20) outliers start: 9 outliers final: 3 residues processed: 104 average time/residue: 0.0765 time to fit residues: 11.2401 Evaluate side-chains 96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 0.9980 chunk 78 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.230094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.203108 restraints weight = 9518.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.203736 restraints weight = 6878.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.205455 restraints weight = 5315.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.206698 restraints weight = 4430.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.207090 restraints weight = 3991.594| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4476 r_free = 0.4476 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4476 r_free = 0.4476 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7766 Z= 0.112 Angle : 0.556 8.703 10502 Z= 0.283 Chirality : 0.043 0.194 1124 Planarity : 0.004 0.052 1374 Dihedral : 4.407 28.815 1032 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.98 % Allowed : 13.66 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.27), residues: 930 helix: 0.27 (0.29), residues: 332 sheet: -1.97 (0.41), residues: 138 loop : -1.09 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 463 TYR 0.023 0.002 TYR B 70 PHE 0.021 0.002 PHE A 173 TRP 0.009 0.001 TRP A 349 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7766) covalent geometry : angle 0.55650 (10502) hydrogen bonds : bond 0.03107 ( 279) hydrogen bonds : angle 5.01367 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.277 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 101 average time/residue: 0.0775 time to fit residues: 11.2510 Evaluate side-chains 94 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 48 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.249613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.223937 restraints weight = 9870.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.223135 restraints weight = 7502.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.224418 restraints weight = 6598.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.224844 restraints weight = 5599.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.225088 restraints weight = 5278.678| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4588 r_free = 0.4588 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4587 r_free = 0.4587 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7766 Z= 0.152 Angle : 0.590 8.971 10502 Z= 0.300 Chirality : 0.044 0.165 1124 Planarity : 0.005 0.048 1374 Dihedral : 4.457 27.422 1032 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.34 % Allowed : 14.76 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.27), residues: 930 helix: 0.06 (0.28), residues: 336 sheet: -2.21 (0.40), residues: 146 loop : -0.96 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 463 TYR 0.019 0.002 TYR B 484 PHE 0.024 0.002 PHE A 173 TRP 0.011 0.002 TRP B 349 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 7766) covalent geometry : angle 0.58960 (10502) hydrogen bonds : bond 0.03281 ( 279) hydrogen bonds : angle 5.08587 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.285 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 102 average time/residue: 0.0682 time to fit residues: 10.1390 Evaluate side-chains 97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 61 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 111 GLN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.250888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.222208 restraints weight = 9872.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.222552 restraints weight = 7509.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.223863 restraints weight = 6235.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.226445 restraints weight = 5059.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.226595 restraints weight = 4567.606| |-----------------------------------------------------------------------------| r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4599 r_free = 0.4599 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4599 r_free = 0.4599 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7766 Z= 0.134 Angle : 0.581 9.233 10502 Z= 0.295 Chirality : 0.043 0.145 1124 Planarity : 0.004 0.051 1374 Dihedral : 4.419 25.912 1032 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.20 % Allowed : 15.73 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.27), residues: 930 helix: 0.10 (0.28), residues: 336 sheet: -2.05 (0.41), residues: 138 loop : -1.01 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 463 TYR 0.018 0.002 TYR B 484 PHE 0.025 0.002 PHE A 173 TRP 0.010 0.002 TRP B 225 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7766) covalent geometry : angle 0.58114 (10502) hydrogen bonds : bond 0.03154 ( 279) hydrogen bonds : angle 5.03555 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.274 Fit side-chains REVERT: A 495 LEU cc_start: 0.4965 (OUTLIER) cc_final: 0.4026 (tp) outliers start: 18 outliers final: 7 residues processed: 104 average time/residue: 0.0778 time to fit residues: 11.5947 Evaluate side-chains 98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 19 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.252198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.224458 restraints weight = 9849.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.225592 restraints weight = 6775.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.226712 restraints weight = 5855.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.227851 restraints weight = 5241.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.227892 restraints weight = 4622.433| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4605 r_free = 0.4605 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4605 r_free = 0.4605 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7766 Z= 0.122 Angle : 0.582 9.518 10502 Z= 0.295 Chirality : 0.043 0.197 1124 Planarity : 0.004 0.050 1374 Dihedral : 4.373 31.015 1032 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.71 % Allowed : 16.10 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.27), residues: 930 helix: 0.11 (0.28), residues: 336 sheet: -2.00 (0.41), residues: 138 loop : -0.96 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 463 TYR 0.023 0.002 TYR A 343 PHE 0.021 0.002 PHE A 173 TRP 0.009 0.001 TRP B 53 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7766) covalent geometry : angle 0.58224 (10502) hydrogen bonds : bond 0.03086 ( 279) hydrogen bonds : angle 5.05933 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.307 Fit side-chains REVERT: A 495 LEU cc_start: 0.4964 (OUTLIER) cc_final: 0.3993 (tp) outliers start: 14 outliers final: 7 residues processed: 102 average time/residue: 0.0816 time to fit residues: 11.8431 Evaluate side-chains 95 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.250858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.220827 restraints weight = 9849.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.224245 restraints weight = 6931.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.226571 restraints weight = 5450.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.227887 restraints weight = 4618.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.229104 restraints weight = 4136.476| |-----------------------------------------------------------------------------| r_work (final): 0.4622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4622 r_free = 0.4622 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4622 r_free = 0.4622 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7766 Z= 0.146 Angle : 0.608 9.654 10502 Z= 0.305 Chirality : 0.044 0.171 1124 Planarity : 0.004 0.046 1374 Dihedral : 4.411 28.810 1032 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.46 % Allowed : 16.34 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.27), residues: 930 helix: 0.01 (0.28), residues: 336 sheet: -2.33 (0.39), residues: 146 loop : -0.86 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 463 TYR 0.019 0.002 TYR B 484 PHE 0.018 0.002 PHE B 253 TRP 0.010 0.002 TRP B 225 HIS 0.002 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7766) covalent geometry : angle 0.60836 (10502) hydrogen bonds : bond 0.03161 ( 279) hydrogen bonds : angle 5.08172 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.275 Fit side-chains REVERT: A 343 TYR cc_start: 0.3649 (m-10) cc_final: 0.3356 (m-80) REVERT: A 495 LEU cc_start: 0.5089 (OUTLIER) cc_final: 0.3656 (tp) REVERT: B 322 TYR cc_start: 0.7718 (t80) cc_final: 0.7415 (t80) outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 0.0822 time to fit residues: 12.2068 Evaluate side-chains 98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 5 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 0.0670 chunk 56 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.250302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.220578 restraints weight = 9881.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.223820 restraints weight = 7019.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.225928 restraints weight = 5499.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.227765 restraints weight = 4657.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.228531 restraints weight = 4138.264| |-----------------------------------------------------------------------------| r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4617 r_free = 0.4617 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4617 r_free = 0.4617 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7766 Z= 0.150 Angle : 0.619 9.308 10502 Z= 0.312 Chirality : 0.045 0.177 1124 Planarity : 0.005 0.048 1374 Dihedral : 4.480 29.189 1032 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.10 % Allowed : 16.46 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.27), residues: 930 helix: -0.09 (0.28), residues: 336 sheet: -2.24 (0.41), residues: 138 loop : -0.99 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 166 TYR 0.019 0.002 TYR B 484 PHE 0.018 0.002 PHE B 216 TRP 0.017 0.002 TRP A 164 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 7766) covalent geometry : angle 0.61867 (10502) hydrogen bonds : bond 0.03170 ( 279) hydrogen bonds : angle 5.11408 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.283 Fit side-chains REVERT: A 343 TYR cc_start: 0.3587 (m-10) cc_final: 0.3320 (m-80) REVERT: A 495 LEU cc_start: 0.5122 (OUTLIER) cc_final: 0.3710 (tp) REVERT: B 322 TYR cc_start: 0.7744 (t80) cc_final: 0.7437 (t80) outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.0799 time to fit residues: 11.2278 Evaluate side-chains 98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.251166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.222746 restraints weight = 9912.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.223510 restraints weight = 7604.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.225238 restraints weight = 6612.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.226281 restraints weight = 5495.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.226314 restraints weight = 4974.639| |-----------------------------------------------------------------------------| r_work (final): 0.4593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4594 r_free = 0.4594 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4594 r_free = 0.4594 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7766 Z= 0.141 Angle : 0.603 9.690 10502 Z= 0.305 Chirality : 0.044 0.198 1124 Planarity : 0.004 0.047 1374 Dihedral : 4.481 30.226 1032 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.22 % Allowed : 17.07 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.27), residues: 930 helix: -0.14 (0.28), residues: 336 sheet: -2.22 (0.41), residues: 138 loop : -0.99 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 463 TYR 0.018 0.002 TYR B 484 PHE 0.018 0.002 PHE B 173 TRP 0.011 0.002 TRP B 164 HIS 0.003 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7766) covalent geometry : angle 0.60299 (10502) hydrogen bonds : bond 0.03137 ( 279) hydrogen bonds : angle 5.10051 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1316.88 seconds wall clock time: 23 minutes 29.90 seconds (1409.90 seconds total)