Starting phenix.real_space_refine on Thu Jul 2 10:19:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ozw_13139/07_2026/7ozw_13139.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ozw_13139/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ozw_13139/07_2026/7ozw_13139.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ozw_13139/07_2026/7ozw_13139.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ozw_13139/07_2026/7ozw_13139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ozw_13139/07_2026/7ozw_13139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ozw_13139/07_2026/7ozw_13139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ozw_13139/07_2026/7ozw_13139.map" } 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-dev-6108/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: 1.63, per 1000 atoms: 0.19 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: 0.70 Conformation dependent library (CDL) restraints added in 420.0 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: 0.88 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: 1.02 Time building geometry restraints manager: 0.94 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=" 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=" O3' DG F 31 " pdb=" P DG F 32 " ideal model delta sigma weight residual 1.607 1.536 0.071 1.50e-02 4.44e+03 2.27e+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: 11934 4.44 - 8.88: 53 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=" N TRP A 535 " pdb=" CA TRP A 535 " pdb=" C TRP A 535 " ideal model delta sigma weight residual 109.07 116.26 -7.19 1.61e+00 3.86e-01 1.99e+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: 0.110 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.170 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.780 ------------------------------------------------------------------------------- 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= 0.300 Angle : 0.838 22.206 11991 Z= 0.494 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 / 0.30 ( 8701) covalent geometry : angle 0.83850 / 0.49 (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 : 0.237 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: 0.0875 time to fit residues: 14.4202 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 : 0.275 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.209035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.167660 restraints weight = 9375.292| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.75 r_work: 0.3791 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8701 Z= 0.206 Angle : 0.681 9.172 11991 Z= 0.356 Chirality : 0.047 0.172 1320 Planarity : 0.005 0.061 1395 Dihedral : 16.229 82.159 1375 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.74 % Allowed : 6.51 % Favored : 92.75 % 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: 0.95 (0.29), residues: 327 sheet: -0.59 (0.40), residues: 143 loop : -0.65 (0.29), 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 0.00476 / 0.21 ( 8701) covalent geometry : angle 0.68071 / 0.36 (11991) hydrogen bonds : bond 0.05388 / 3.47 ( 343) hydrogen bonds : angle 5.44225 / 3.86 ( 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 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 232 TYR cc_start: 0.8088 (m-10) cc_final: 0.7705 (m-10) REVERT: A 476 LYS cc_start: 0.6491 (mptt) cc_final: 0.5607 (mttt) REVERT: B 198 HIS cc_start: 0.7059 (t70) cc_final: 0.6808 (t70) REVERT: B 342 TYR cc_start: 0.7707 (p90) cc_final: 0.7354 (p90) outliers start: 6 outliers final: 4 residues processed: 124 average time/residue: 0.0790 time to fit residues: 13.4424 Evaluate side-chains 109 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 57 ASN 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: 5.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 3 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 428 GLN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.208129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.168487 restraints weight = 9389.449| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.85 r_work: 0.3769 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8701 Z= 0.195 Angle : 0.644 8.536 11991 Z= 0.340 Chirality : 0.045 0.152 1320 Planarity : 0.005 0.055 1395 Dihedral : 16.453 82.038 1375 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.47 % Allowed : 10.44 % Favored : 88.08 % 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: -0.26 (0.27), residues: 955 helix: 0.93 (0.29), residues: 327 sheet: -0.81 (0.40), residues: 143 loop : -0.69 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 143 TYR 0.015 0.002 TYR B 181 PHE 0.016 0.002 PHE B 130 TRP 0.021 0.002 TRP A 402 HIS 0.008 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 8701) covalent geometry : angle 0.64439 / 0.34 (11991) hydrogen bonds : bond 0.04820 / 3.06 ( 343) hydrogen bonds : angle 5.14798 / 3.66 ( 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 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 194 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6608 (pm20) REVERT: B 201 LYS cc_start: 0.7092 (tttm) cc_final: 0.6857 (tttt) REVERT: B 342 TYR cc_start: 0.7530 (p90) cc_final: 0.7161 (p90) outliers start: 12 outliers final: 7 residues processed: 121 average time/residue: 0.0733 time to fit residues: 12.2670 Evaluate side-chains 113 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 57 ASN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 38 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 97 optimal weight: 50.0000 chunk 80 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.207521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.167973 restraints weight = 9581.273| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.85 r_work: 0.3751 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8701 Z= 0.196 Angle : 0.643 8.416 11991 Z= 0.339 Chirality : 0.045 0.153 1320 Planarity : 0.005 0.052 1395 Dihedral : 16.512 82.065 1375 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.72 % Allowed : 13.39 % Favored : 84.89 % 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: -0.39 (0.27), residues: 955 helix: 0.90 (0.29), residues: 326 sheet: -0.90 (0.40), residues: 143 loop : -0.82 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 143 TYR 0.016 0.002 TYR A 181 PHE 0.017 0.002 PHE B 130 TRP 0.024 0.002 TRP A 402 HIS 0.009 0.002 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 ( 8701) covalent geometry : angle 0.64253 / 0.34 (11991) hydrogen bonds : bond 0.04627 / 2.96 ( 343) hydrogen bonds : angle 5.08604 / 3.62 ( 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: 14 poor density : 110 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 184 MET cc_start: 0.6655 (mmt) cc_final: 0.6376 (tpt) REVERT: A 269 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6970 (mp10) REVERT: A 469 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7428 (mp) REVERT: B 194 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6396 (tm-30) REVERT: B 342 TYR cc_start: 0.7515 (p90) cc_final: 0.7141 (p90) outliers start: 14 outliers final: 9 residues processed: 119 average time/residue: 0.0768 time to fit residues: 12.8036 Evaluate side-chains 118 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 A residue 469 LEU Chi-restraints excluded: chain B residue 31 ILE 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 380 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 57 ASN B 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.211745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.171921 restraints weight = 9455.329| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.90 r_work: 0.3796 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8701 Z= 0.131 Angle : 0.587 8.050 11991 Z= 0.310 Chirality : 0.043 0.150 1320 Planarity : 0.004 0.049 1395 Dihedral : 16.344 81.848 1375 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.97 % Allowed : 15.11 % 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: -0.05 (0.28), residues: 955 helix: 1.26 (0.29), residues: 327 sheet: -0.69 (0.40), residues: 142 loop : -0.68 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 143 TYR 0.013 0.001 TYR A 232 PHE 0.013 0.001 PHE B 130 TRP 0.021 0.001 TRP A 402 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8701) covalent geometry : angle 0.58676 / 0.31 (11991) hydrogen bonds : bond 0.03917 / 2.48 ( 343) hydrogen bonds : angle 4.87660 / 3.49 ( 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 135 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.285 Fit side-chains REVERT: A 184 MET cc_start: 0.6711 (mmt) cc_final: 0.6445 (tpt) REVERT: A 269 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6862 (mp10) REVERT: A 469 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7369 (mp) REVERT: B 194 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6529 (pm20) REVERT: B 342 TYR cc_start: 0.7436 (p90) cc_final: 0.7090 (p90) outliers start: 16 outliers final: 7 residues processed: 130 average time/residue: 0.0838 time to fit residues: 14.8470 Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 A residue 469 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- 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 ** B 198 HIS ** 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 = 0.4365 r_free = 0.4365 target = 0.206641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.167375 restraints weight = 9304.267| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.86 r_work: 0.3741 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8701 Z= 0.236 Angle : 0.690 8.725 11991 Z= 0.363 Chirality : 0.047 0.163 1320 Planarity : 0.005 0.051 1395 Dihedral : 16.484 82.000 1375 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.60 % Allowed : 16.46 % Favored : 81.94 % 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: -0.51 (0.27), residues: 955 helix: 0.78 (0.29), residues: 326 sheet: -0.87 (0.41), residues: 143 loop : -0.91 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.018 0.002 TYR A 232 PHE 0.019 0.002 PHE B 130 TRP 0.028 0.002 TRP A 402 HIS 0.010 0.002 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 ( 8701) covalent geometry : angle 0.69038 / 0.36 (11991) hydrogen bonds : bond 0.04817 / 3.07 ( 343) hydrogen bonds : angle 5.08631 / 3.62 ( 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 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 184 MET cc_start: 0.6952 (mmt) cc_final: 0.6623 (tpt) REVERT: A 269 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: B 138 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: B 194 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6777 (tm-30) REVERT: B 342 TYR cc_start: 0.7626 (p90) cc_final: 0.7206 (p90) outliers start: 13 outliers final: 7 residues processed: 120 average time/residue: 0.0768 time to fit residues: 12.4659 Evaluate side-chains 114 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.209682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.169759 restraints weight = 9442.794| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.87 r_work: 0.3771 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8701 Z= 0.152 Angle : 0.631 8.050 11991 Z= 0.330 Chirality : 0.044 0.147 1320 Planarity : 0.005 0.049 1395 Dihedral : 16.358 82.264 1375 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.72 % Allowed : 17.44 % Favored : 80.84 % 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: -0.25 (0.27), residues: 955 helix: 1.12 (0.29), residues: 325 sheet: -0.74 (0.41), residues: 143 loop : -0.84 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 125 TYR 0.013 0.002 TYR A 232 PHE 0.015 0.001 PHE B 130 TRP 0.033 0.002 TRP B 402 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8701) covalent geometry : angle 0.63063 / 0.33 (11991) hydrogen bonds : bond 0.04071 / 2.59 ( 343) hydrogen bonds : angle 4.91894 / 3.52 ( 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 126 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 184 MET cc_start: 0.6928 (mmt) cc_final: 0.6600 (tpt) REVERT: A 269 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6783 (mp10) REVERT: A 358 ARG cc_start: 0.7102 (mmt90) cc_final: 0.6851 (mmm160) REVERT: A 373 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 194 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6829 (tm-30) REVERT: B 342 TYR cc_start: 0.7527 (p90) cc_final: 0.7147 (p90) outliers start: 14 outliers final: 9 residues processed: 124 average time/residue: 0.0796 time to fit residues: 13.7390 Evaluate side-chains 119 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 175 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 414 TRP 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: 10.0000 chunk 37 optimal weight: 1.9990 chunk 97 optimal weight: 50.0000 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** B 198 HIS ** 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 = 0.4385 r_free = 0.4385 target = 0.208786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.168802 restraints weight = 9373.569| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.85 r_work: 0.3758 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8701 Z= 0.171 Angle : 0.645 8.403 11991 Z= 0.337 Chirality : 0.044 0.158 1320 Planarity : 0.005 0.048 1395 Dihedral : 16.346 82.292 1375 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.60 % Allowed : 17.69 % Favored : 80.71 % 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: -0.31 (0.27), residues: 955 helix: 1.07 (0.29), residues: 326 sheet: -0.81 (0.41), residues: 147 loop : -0.87 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.015 0.002 TYR A 232 PHE 0.015 0.001 PHE B 130 TRP 0.039 0.002 TRP B 402 HIS 0.006 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 8701) covalent geometry : angle 0.64498 / 0.34 (11991) hydrogen bonds : bond 0.04181 / 2.65 ( 343) hydrogen bonds : angle 4.94412 / 3.53 ( 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 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 184 MET cc_start: 0.7150 (mmt) cc_final: 0.6814 (tpt) REVERT: A 269 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: A 358 ARG cc_start: 0.7236 (mmt90) cc_final: 0.6849 (mmm160) REVERT: A 373 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 138 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: B 194 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6770 (tm-30) REVERT: B 342 TYR cc_start: 0.7782 (p90) cc_final: 0.7422 (p90) outliers start: 13 outliers final: 9 residues processed: 121 average time/residue: 0.0781 time to fit residues: 13.1015 Evaluate side-chains 118 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 201 LYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 414 TRP 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: 6.9990 chunk 21 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 82 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.211571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.170980 restraints weight = 9388.607| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.76 r_work: 0.3806 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8701 Z= 0.127 Angle : 0.606 8.430 11991 Z= 0.317 Chirality : 0.043 0.146 1320 Planarity : 0.005 0.048 1395 Dihedral : 16.221 82.107 1375 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.47 % Allowed : 18.18 % Favored : 80.34 % 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: -0.06 (0.28), residues: 955 helix: 1.34 (0.29), residues: 326 sheet: -0.63 (0.42), residues: 138 loop : -0.79 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 125 TYR 0.011 0.001 TYR A 232 PHE 0.013 0.001 PHE B 130 TRP 0.028 0.001 TRP B 402 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8701) covalent geometry : angle 0.60589 / 0.32 (11991) hydrogen bonds : bond 0.03730 / 2.36 ( 343) hydrogen bonds : angle 4.81718 / 3.45 ( 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 129 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.5417 (pm20) cc_final: 0.5160 (tp30) REVERT: A 102 LYS cc_start: 0.6063 (mmmt) cc_final: 0.5726 (tppt) REVERT: A 184 MET cc_start: 0.7082 (mmt) cc_final: 0.6750 (tpt) REVERT: A 269 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6752 (mp10) REVERT: A 358 ARG cc_start: 0.7178 (mmt90) cc_final: 0.6748 (mmm160) REVERT: A 373 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8135 (tm-30) REVERT: B 138 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: B 194 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6781 (tm-30) REVERT: B 342 TYR cc_start: 0.7726 (p90) cc_final: 0.7381 (p90) outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 0.0743 time to fit residues: 13.0879 Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 189 VAL Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 414 TRP 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 43 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 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 A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.207872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.166841 restraints weight = 9413.860| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.78 r_work: 0.3758 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2056 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= 0.201 Angle : 0.674 9.069 11991 Z= 0.350 Chirality : 0.046 0.204 1320 Planarity : 0.005 0.048 1395 Dihedral : 16.320 82.429 1375 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.47 % Allowed : 18.18 % Favored : 80.34 % 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: -0.33 (0.27), residues: 955 helix: 1.03 (0.29), residues: 326 sheet: -0.81 (0.41), residues: 147 loop : -0.87 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 125 TYR 0.015 0.002 TYR B 181 PHE 0.017 0.002 PHE B 130 TRP 0.026 0.002 TRP A 402 HIS 0.009 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 8701) covalent geometry : angle 0.67394 / 0.35 (11991) hydrogen bonds : bond 0.04381 / 2.79 ( 343) hydrogen bonds : angle 4.97831 / 3.54 ( 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 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.182 Fit side-chains REVERT: A 79 GLU cc_start: 0.5590 (pm20) cc_final: 0.5181 (tp30) REVERT: A 184 MET cc_start: 0.7125 (mmt) cc_final: 0.6809 (tpt) REVERT: A 269 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: A 358 ARG cc_start: 0.7186 (mmt90) cc_final: 0.6819 (mmm160) REVERT: A 373 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 138 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: B 194 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6842 (tm-30) REVERT: B 342 TYR cc_start: 0.7823 (p90) cc_final: 0.7485 (p90) outliers start: 12 outliers final: 6 residues processed: 121 average time/residue: 0.0716 time to fit residues: 12.0257 Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 189 VAL 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: 0.0570 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.212390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.172197 restraints weight = 9314.460| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.78 r_work: 0.3800 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8701 Z= 0.122 Angle : 0.609 8.897 11991 Z= 0.319 Chirality : 0.043 0.149 1320 Planarity : 0.005 0.047 1395 Dihedral : 16.144 82.304 1375 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.98 % Allowed : 18.80 % Favored : 80.22 % 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: -0.01 (0.28), residues: 955 helix: 1.36 (0.30), residues: 326 sheet: -0.61 (0.41), residues: 144 loop : -0.74 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 125 TYR 0.019 0.001 TYR B 181 PHE 0.012 0.001 PHE A 160 TRP 0.025 0.001 TRP A 229 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8701) covalent geometry : angle 0.60918 / 0.32 (11991) hydrogen bonds : bond 0.03652 / 2.32 ( 343) hydrogen bonds : angle 4.81642 / 3.44 ( 928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.52 seconds wall clock time: 27 minutes 50.61 seconds (1670.61 seconds total)