Starting phenix.real_space_refine on Fri Sep 11 06:47:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ozw_13139/09_2026/7ozw_13139.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ozw_13139/09_2026/7ozw_13139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ozw_13139/09_2026/7ozw_13139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ozw_13139/09_2026/7ozw_13139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ozw_13139/09_2026/7ozw_13139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ozw_13139/09_2026/7ozw_13139.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ozw_13139/09_2026/7ozw_13139.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ozw_13139/09_2026/7ozw_13139.cif" } resolution = 3.38 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= 0.020 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 P 34 5.49 5 S 14 5.16 5 C 5341 2.51 5 N 1404 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8407 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4388 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 514} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3303 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 29, 'TRANS': 379} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 699 Classifications: {'DNA': 32, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 33} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'3IR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.75, per 1000 atoms: 0.21 Number of scatterers: 8407 At special positions: 0 Unit cell: (94.09, 99.91, 102.82, 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 14 16.00 P 34 15.00 O 1614 8.00 N 1404 7.00 C 5341 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: 0.85 Conformation dependent library (CDL) restraints added in 284.0 milliseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 37.8% alpha, 14.2% beta 11 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.955A pdb=" N THR A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 removed outlier: 4.172A pdb=" N LYS A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.716A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.646A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 363 through 384 removed outlier: 3.524A pdb=" N THR A 377 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.550A pdb=" N SER A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'B' and resid 27 through 44 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.753A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 removed outlier: 4.688A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.984A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 213 removed outlier: 3.633A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.544A pdb=" N TRP B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.946A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 283 removed outlier: 3.695A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 363 through 384 Processing helix chain 'B' and resid 394 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 removed outlier: 3.545A pdb=" N TYR A 183 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.730A pdb=" N LYS A 238 " --> pdb=" O HIS A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 354 removed outlier: 8.353A pdb=" N ASN A 348 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN A 343 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.716A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.793A pdb=" N LEU A 452 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLU A 438 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL A 496 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.531A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.803A pdb=" N PHE B 130 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.906A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 350 through 355 removed outlier: 3.635A pdb=" N TYR B 339 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1323 1.32 - 1.44: 2426 1.44 - 1.56: 4858 1.56 - 1.69: 68 1.69 - 1.81: 26 Bond restraints: 8701 Sorted by residual: bond pdb=" C4' DC F 10 " pdb=" O4' DC F 10 " ideal model delta sigma weight residual 1.446 1.555 -0.109 1.00e-02 1.00e+04 1.19e+02 bond pdb=" O3' DG F 31 " pdb=" P DG F 32 " ideal model delta sigma weight residual 1.607 1.536 0.071 1.20e-02 6.94e+03 3.54e+01 bond pdb=" C5 3IR A 601 " pdb=" C7 3IR A 601 " ideal model delta sigma weight residual 1.526 1.629 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C1 3IR A 601 " pdb=" C5 3IR A 601 " ideal model delta sigma weight residual 1.483 1.585 -0.102 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C1 3IR A 601 " pdb=" N1 3IR A 601 " ideal model delta sigma weight residual 1.373 1.465 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 8696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 11933 4.44 - 8.88: 54 8.88 - 13.32: 2 13.32 - 17.76: 1 17.76 - 22.21: 1 Bond angle restraints: 11991 Sorted by residual: angle pdb=" C5' DC F 10 " pdb=" C4' DC F 10 " pdb=" O4' DC F 10 " ideal model delta sigma weight residual 109.30 131.51 -22.21 1.90e+00 2.77e-01 1.37e+02 angle pdb=" O4' DC F 10 " pdb=" C4' DC F 10 " pdb=" C3' DC F 10 " ideal model delta sigma weight residual 106.00 101.06 4.94 6.00e-01 2.78e+00 6.78e+01 angle pdb=" C5 3IR A 601 " pdb=" C7 3IR A 601 " pdb=" C8 3IR A 601 " ideal model delta sigma weight residual 120.05 136.38 -16.33 3.00e+00 1.11e-01 2.96e+01 angle pdb=" N ILE A 180 " pdb=" CA ILE A 180 " pdb=" C ILE A 180 " ideal model delta sigma weight residual 106.61 115.90 -9.29 1.78e+00 3.16e-01 2.73e+01 angle pdb=" C3' DG F 31 " pdb=" O3' DG F 31 " pdb=" P DG F 32 " ideal model delta sigma weight residual 119.70 125.61 -5.91 1.20e+00 6.94e-01 2.43e+01 ... (remaining 11986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4391 17.89 - 35.77: 509 35.77 - 53.66: 143 53.66 - 71.55: 36 71.55 - 89.43: 9 Dihedral angle restraints: 5088 sinusoidal: 2281 harmonic: 2807 Sorted by residual: dihedral pdb=" CA VAL B 423 " pdb=" C VAL B 423 " pdb=" N LYS B 424 " pdb=" CA LYS B 424 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA VAL A 35 " pdb=" C VAL A 35 " pdb=" N GLU A 36 " pdb=" CA GLU A 36 " ideal model delta harmonic sigma weight residual -180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASP B 86 " pdb=" C ASP B 86 " pdb=" N PHE B 87 " pdb=" CA PHE B 87 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1303 0.154 - 0.307: 14 0.307 - 0.461: 2 0.461 - 0.614: 0 0.614 - 0.768: 1 Chirality restraints: 1320 Sorted by residual: chirality pdb=" C4' DC F 10 " pdb=" C5' DC F 10 " pdb=" O4' DC F 10 " pdb=" C3' DC F 10 " both_signs ideal model delta sigma weight residual False -2.53 -1.76 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" CA PHE B 77 " pdb=" N PHE B 77 " pdb=" C PHE B 77 " pdb=" CB PHE B 77 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C4' DG F 24 " pdb=" C5' DG F 24 " pdb=" O4' DG F 24 " pdb=" C3' DG F 24 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 1317 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 312 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO B 313 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 125 " -0.205 9.50e-02 1.11e+02 9.20e-02 5.20e+00 pdb=" NE ARG B 125 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 125 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 125 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 125 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 414 " 0.011 2.00e-02 2.50e+03 1.11e-02 3.08e+00 pdb=" CG TRP B 414 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 414 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 414 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 414 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 414 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 414 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 414 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 414 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 414 " 0.002 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2069 2.80 - 3.33: 7487 3.33 - 3.85: 14044 3.85 - 4.38: 16326 4.38 - 4.90: 27492 Nonbonded interactions: 67418 Sorted by model distance: nonbonded pdb=" NH1 ARG A 277 " pdb=" O ALA A 355 " model vdw 2.276 3.120 nonbonded pdb=" OG1 THR A 107 " pdb=" NE2 HIS A 198 " model vdw 2.308 3.120 nonbonded pdb=" O TYR A 427 " pdb=" NE2 GLN A 509 " model vdw 2.323 3.120 nonbonded pdb=" NZ LYS B 73 " pdb=" OH TYR B 146 " model vdw 2.328 3.120 nonbonded pdb=" OG1 THR A 403 " pdb=" OE1 GLU A 404 " model vdw 2.329 3.040 ... (remaining 67413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.220 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 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 : 0.005 0.109 8701 Z= 0.309 Angle : 0.841 22.206 11991 Z= 0.499 Chirality : 0.057 0.768 1320 Planarity : 0.005 0.092 1395 Dihedral : 16.830 89.432 3278 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.27 (0.27), residues: 955 helix: 0.76 (0.29), residues: 326 sheet: 0.00 (0.42), residues: 126 loop : -0.83 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 358 TYR 0.017 0.001 TYR A 532 PHE 0.010 0.001 PHE A 160 TRP 0.029 0.001 TRP B 414 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.31 ( 8701) covalent geometry : angle 0.84115 / 0.50 (11991) hydrogen bonds : bond 0.17032 / 10.51 ( 343) hydrogen bonds : angle 7.85879 / 5.50 ( 928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.7487 (tm-30) cc_final: 0.7188 (tm-30) REVERT: B 287 LYS cc_start: 0.7461 (mppt) cc_final: 0.7113 (mmtp) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1063 time to fit residues: 17.3942 Evaluate side-chains 101 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 50.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.208804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.167351 restraints weight = 9381.478| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.75 r_work: 0.3776 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8701 Z= 0.209 Angle : 0.682 9.236 11991 Z= 0.357 Chirality : 0.047 0.178 1320 Planarity : 0.005 0.060 1395 Dihedral : 16.239 81.839 1375 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.74 % Allowed : 6.76 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.19 (0.27), residues: 955 helix: 0.94 (0.29), residues: 327 sheet: -0.61 (0.39), residues: 143 loop : -0.66 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 143 TYR 0.017 0.002 TYR B 181 PHE 0.018 0.002 PHE B 130 TRP 0.016 0.002 TRP A 402 HIS 0.007 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 ( 8701) covalent geometry : angle 0.68172 / 0.36 (11991) hydrogen bonds : bond 0.05295 / 3.40 ( 343) hydrogen bonds : angle 5.41010 / 3.84 ( 928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 TYR cc_start: 0.8078 (m-10) cc_final: 0.7713 (m-10) REVERT: A 476 LYS cc_start: 0.6494 (mptt) cc_final: 0.5645 (mttt) REVERT: B 342 TYR cc_start: 0.7682 (p90) cc_final: 0.7294 (p90) outliers start: 6 outliers final: 3 residues processed: 123 average time/residue: 0.0858 time to fit residues: 14.5406 Evaluate side-chains 107 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 189 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 84 optimal weight: 0.0070 chunk 39 optimal weight: 6.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.211413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.172000 restraints weight = 9292.557| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.87 r_work: 0.3796 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8701 Z= 0.147 Angle : 0.601 8.194 11991 Z= 0.317 Chirality : 0.044 0.149 1320 Planarity : 0.005 0.053 1395 Dihedral : 16.365 81.576 1375 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.23 % Allowed : 9.83 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.03 (0.27), residues: 955 helix: 1.20 (0.29), residues: 327 sheet: -0.68 (0.40), residues: 143 loop : -0.61 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 143 TYR 0.013 0.002 TYR B 181 PHE 0.013 0.001 PHE B 130 TRP 0.018 0.001 TRP A 402 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8701) covalent geometry : angle 0.60114 / 0.32 (11991) hydrogen bonds : bond 0.04395 / 2.78 ( 343) hydrogen bonds : angle 5.05989 / 3.60 ( 928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.270 Fit side-chains REVERT: A 373 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 469 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6779 (mp) REVERT: A 476 LYS cc_start: 0.6349 (mptt) cc_final: 0.5526 (mttt) REVERT: B 194 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6541 (pm20) REVERT: B 342 TYR cc_start: 0.7479 (p90) cc_final: 0.7145 (p90) outliers start: 10 outliers final: 7 residues processed: 122 average time/residue: 0.0820 time to fit residues: 13.8955 Evaluate side-chains 114 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 414 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 38 optimal weight: 0.0980 chunk 48 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 97 optimal weight: 50.0000 chunk 80 optimal weight: 20.0000 chunk 54 optimal weight: 0.4980 chunk 2 optimal weight: 30.0000 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 428 GLN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** 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 = 0.4384 r_free = 0.4384 target = 0.208898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.169970 restraints weight = 9496.271| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.85 r_work: 0.3761 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8701 Z= 0.190 Angle : 0.636 8.275 11991 Z= 0.335 Chirality : 0.045 0.152 1320 Planarity : 0.005 0.051 1395 Dihedral : 16.464 82.380 1375 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.35 % Allowed : 12.78 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.21 (0.27), residues: 955 helix: 1.06 (0.29), residues: 326 sheet: -0.76 (0.40), residues: 142 loop : -0.74 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 143 TYR 0.017 0.002 TYR A 181 PHE 0.016 0.002 PHE B 130 TRP 0.023 0.002 TRP A 402 HIS 0.008 0.002 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 8701) covalent geometry : angle 0.63578 / 0.34 (11991) hydrogen bonds : bond 0.04498 / 2.86 ( 343) hydrogen bonds : angle 5.05662 / 3.60 ( 928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.284 Fit side-chains REVERT: A 184 MET cc_start: 0.6615 (mmt) cc_final: 0.6326 (tpt) REVERT: A 269 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6980 (mp10) REVERT: B 194 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6442 (tm-30) REVERT: B 342 TYR cc_start: 0.7506 (p90) cc_final: 0.7130 (p90) outliers start: 11 outliers final: 8 residues processed: 120 average time/residue: 0.0793 time to fit residues: 13.4364 Evaluate side-chains 113 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 414 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 76 optimal weight: 0.0270 chunk 58 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN ** B 198 HIS ** 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 = 0.4433 r_free = 0.4433 target = 0.214539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.174497 restraints weight = 9364.435| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.80 r_work: 0.3843 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8701 Z= 0.111 Angle : 0.568 7.550 11991 Z= 0.300 Chirality : 0.043 0.151 1320 Planarity : 0.004 0.047 1395 Dihedral : 16.238 82.681 1375 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.11 % Allowed : 14.25 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.16 (0.28), residues: 955 helix: 1.52 (0.30), residues: 327 sheet: -0.61 (0.41), residues: 138 loop : -0.63 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 143 TYR 0.016 0.001 TYR A 232 PHE 0.011 0.001 PHE A 160 TRP 0.019 0.001 TRP A 402 HIS 0.015 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 8701) covalent geometry : angle 0.56834 / 0.30 (11991) hydrogen bonds : bond 0.03551 / 2.24 ( 343) hydrogen bonds : angle 4.82509 / 3.46 ( 928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 184 MET cc_start: 0.6480 (mmt) cc_final: 0.6210 (tpt) REVERT: A 232 TYR cc_start: 0.7705 (m-10) cc_final: 0.7400 (m-10) REVERT: A 269 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6749 (mp10) REVERT: A 469 LEU cc_start: 0.7564 (mp) cc_final: 0.7169 (mp) REVERT: A 476 LYS cc_start: 0.6316 (mptt) cc_final: 0.5529 (mttt) REVERT: B 194 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6506 (pm20) REVERT: B 342 TYR cc_start: 0.7407 (p90) cc_final: 0.7091 (p90) outliers start: 9 outliers final: 5 residues processed: 120 average time/residue: 0.0933 time to fit residues: 15.2578 Evaluate side-chains 113 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 414 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.207905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.167344 restraints weight = 9343.236| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.78 r_work: 0.3756 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8701 Z= 0.207 Angle : 0.650 8.225 11991 Z= 0.341 Chirality : 0.045 0.151 1320 Planarity : 0.005 0.048 1395 Dihedral : 16.357 83.319 1375 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.60 % Allowed : 14.86 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.18 (0.27), residues: 955 helix: 1.12 (0.29), residues: 326 sheet: -0.76 (0.40), residues: 145 loop : -0.73 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.021 0.002 TYR B 181 PHE 0.017 0.002 PHE B 130 TRP 0.027 0.002 TRP A 402 HIS 0.010 0.002 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 ( 8701) covalent geometry : angle 0.64977 / 0.34 (11991) hydrogen bonds : bond 0.04527 / 2.87 ( 343) hydrogen bonds : angle 4.93801 / 3.52 ( 928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.218 Fit side-chains REVERT: A 184 MET cc_start: 0.7014 (mmt) cc_final: 0.6749 (tpt) REVERT: A 269 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: B 194 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6651 (tm-30) REVERT: B 342 TYR cc_start: 0.7821 (p90) cc_final: 0.7414 (p90) outliers start: 13 outliers final: 9 residues processed: 116 average time/residue: 0.0794 time to fit residues: 12.9483 Evaluate side-chains 114 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.210052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.170242 restraints weight = 9451.036| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.91 r_work: 0.3769 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8701 Z= 0.150 Angle : 0.616 8.069 11991 Z= 0.323 Chirality : 0.044 0.144 1320 Planarity : 0.005 0.047 1395 Dihedral : 16.276 82.530 1375 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.35 % Allowed : 15.72 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.04 (0.28), residues: 955 helix: 1.24 (0.29), residues: 327 sheet: -0.69 (0.40), residues: 145 loop : -0.65 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 143 TYR 0.018 0.002 TYR B 181 PHE 0.013 0.001 PHE B 130 TRP 0.024 0.001 TRP A 402 HIS 0.006 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 8701) covalent geometry : angle 0.61552 / 0.32 (11991) hydrogen bonds : bond 0.04029 / 2.57 ( 343) hydrogen bonds : angle 4.84167 / 3.46 ( 928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.301 Fit side-chains REVERT: A 184 MET cc_start: 0.6855 (mmt) cc_final: 0.6558 (tpt) REVERT: A 269 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6783 (mp10) REVERT: A 373 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7998 (tm-30) REVERT: B 194 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6774 (tm-30) REVERT: B 342 TYR cc_start: 0.7533 (p90) cc_final: 0.7164 (p90) outliers start: 11 outliers final: 6 residues processed: 116 average time/residue: 0.0817 time to fit residues: 13.2097 Evaluate side-chains 112 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 380 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 40.0000 chunk 45 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 97 optimal weight: 50.0000 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 84 optimal weight: 0.0980 chunk 13 optimal weight: 9.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 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 = 0.4372 r_free = 0.4372 target = 0.207275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.167971 restraints weight = 9386.430| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.89 r_work: 0.3739 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8701 Z= 0.206 Angle : 0.666 9.189 11991 Z= 0.349 Chirality : 0.045 0.149 1320 Planarity : 0.005 0.048 1395 Dihedral : 16.354 82.436 1375 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.23 % Allowed : 16.09 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.38 (0.27), residues: 955 helix: 0.89 (0.29), residues: 327 sheet: -0.82 (0.40), residues: 148 loop : -0.82 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.018 0.002 TYR B 181 PHE 0.016 0.002 PHE B 130 TRP 0.027 0.002 TRP A 402 HIS 0.009 0.002 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 ( 8701) covalent geometry : angle 0.66599 / 0.35 (11991) hydrogen bonds : bond 0.04504 / 2.87 ( 343) hydrogen bonds : angle 4.96992 / 3.54 ( 928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.293 Fit side-chains REVERT: A 184 MET cc_start: 0.6926 (mmt) cc_final: 0.6589 (tpt) REVERT: A 269 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7027 (mp10) REVERT: A 373 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8101 (tm-30) REVERT: B 138 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: B 194 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6791 (tm-30) REVERT: B 342 TYR cc_start: 0.7610 (p90) cc_final: 0.7255 (p90) outliers start: 10 outliers final: 7 residues processed: 117 average time/residue: 0.0819 time to fit residues: 13.3174 Evaluate side-chains 113 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 72 optimal weight: 0.2980 chunk 82 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 92 optimal weight: 0.0670 overall best weight: 3.0724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.209857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.169282 restraints weight = 9344.763| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.78 r_work: 0.3770 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8701 Z= 0.149 Angle : 0.625 8.673 11991 Z= 0.329 Chirality : 0.044 0.144 1320 Planarity : 0.005 0.048 1395 Dihedral : 16.281 81.856 1375 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.23 % Allowed : 17.08 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.19 (0.27), residues: 955 helix: 1.11 (0.29), residues: 327 sheet: -0.75 (0.41), residues: 141 loop : -0.75 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 143 TYR 0.017 0.002 TYR B 181 PHE 0.013 0.001 PHE A 160 TRP 0.039 0.002 TRP B 402 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 8701) covalent geometry : angle 0.62479 / 0.33 (11991) hydrogen bonds : bond 0.04000 / 2.55 ( 343) hydrogen bonds : angle 4.86613 / 3.48 ( 928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.235 Fit side-chains REVERT: A 184 MET cc_start: 0.7088 (mmt) cc_final: 0.6764 (tpt) REVERT: A 269 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: A 373 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8222 (tm-30) REVERT: B 138 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: B 194 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6778 (tm-30) REVERT: B 342 TYR cc_start: 0.7733 (p90) cc_final: 0.7420 (p90) outliers start: 10 outliers final: 7 residues processed: 120 average time/residue: 0.0903 time to fit residues: 14.8875 Evaluate side-chains 118 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 380 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 43 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 97 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.207351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.167244 restraints weight = 9418.360| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.87 r_work: 0.3740 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8701 Z= 0.204 Angle : 0.695 11.174 11991 Z= 0.362 Chirality : 0.046 0.162 1320 Planarity : 0.005 0.049 1395 Dihedral : 16.365 82.051 1375 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.35 % Allowed : 16.95 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.45 (0.27), residues: 955 helix: 0.83 (0.29), residues: 325 sheet: -0.82 (0.41), residues: 148 loop : -0.87 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.017 0.002 TYR B 181 PHE 0.015 0.002 PHE B 87 TRP 0.048 0.002 TRP B 402 HIS 0.008 0.002 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 ( 8701) covalent geometry : angle 0.69465 / 0.36 (11991) hydrogen bonds : bond 0.04470 / 2.85 ( 343) hydrogen bonds : angle 5.04236 / 3.58 ( 928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.229 Fit side-chains REVERT: A 102 LYS cc_start: 0.6188 (mmmt) cc_final: 0.5929 (tppt) REVERT: A 184 MET cc_start: 0.6987 (mmt) cc_final: 0.6645 (tpt) REVERT: A 269 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: B 138 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: B 194 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6863 (tm-30) REVERT: B 342 TYR cc_start: 0.7599 (p90) cc_final: 0.7254 (p90) outliers start: 11 outliers final: 8 residues processed: 116 average time/residue: 0.0762 time to fit residues: 12.5282 Evaluate side-chains 114 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 21 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 174 GLN ** B 175 ASN ** 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 = 0.4401 r_free = 0.4401 target = 0.210524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.168804 restraints weight = 9286.559| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.72 r_work: 0.3795 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8701 Z= 0.138 Angle : 0.629 9.757 11991 Z= 0.330 Chirality : 0.043 0.149 1320 Planarity : 0.005 0.048 1395 Dihedral : 16.228 81.868 1375 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.11 % Allowed : 17.57 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.17 (0.27), residues: 955 helix: 1.17 (0.30), residues: 325 sheet: -0.70 (0.42), residues: 140 loop : -0.79 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 143 TYR 0.017 0.001 TYR B 181 PHE 0.013 0.001 PHE A 160 TRP 0.038 0.002 TRP B 402 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 8701) covalent geometry : angle 0.62898 / 0.33 (11991) hydrogen bonds : bond 0.03877 / 2.48 ( 343) hydrogen bonds : angle 4.91307 / 3.51 ( 928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1766.26 seconds wall clock time: 30 minutes 59.34 seconds (1859.34 seconds total)