Starting phenix.real_space_refine on Tue Feb 13 07:47:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbn_34638/02_2024/8hbn_34638.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbn_34638/02_2024/8hbn_34638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbn_34638/02_2024/8hbn_34638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbn_34638/02_2024/8hbn_34638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbn_34638/02_2024/8hbn_34638.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbn_34638/02_2024/8hbn_34638.pdb" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2668 2.51 5 N 722 2.21 5 O 781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A GLU 410": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4189 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2909 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 16, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1280 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 2.77, per 1000 atoms: 0.66 Number of scatterers: 4189 At special positions: 0 Unit cell: (70.808, 97.528, 85.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 781 8.00 N 722 7.00 C 2668 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 785.9 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 32.1% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 101 through 114 removed outlier: 3.972A pdb=" N PHE A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.586A pdb=" N ILE A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 135' Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.806A pdb=" N MET A 152 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N MET A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 184 removed outlier: 5.087A pdb=" N THR A 182 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 184 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.667A pdb=" N TRP A 209 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 230 removed outlier: 5.903A pdb=" N LYS A 230 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.819A pdb=" N GLU A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 removed outlier: 3.657A pdb=" N VAL A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.537A pdb=" N ASN A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.715A pdb=" N LEU A 300 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 301 " --> pdb=" O GLN A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 301' Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.682A pdb=" N MET A 335 " --> pdb=" O GLY A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.711A pdb=" N GLN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 368 removed outlier: 3.861A pdb=" N THR A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 31 removed outlier: 3.797A pdb=" N ILE B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 removed outlier: 4.085A pdb=" N PHE B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 37 through 45' Processing helix chain 'B' and resid 61 through 72 removed outlier: 3.656A pdb=" N PHE B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 72 " --> pdb=" O MET B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 6.578A pdb=" N LEU A 122 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 167 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A 193 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 removed outlier: 6.704A pdb=" N PHE A 271 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N SER A 388 " --> pdb=" O PHE A 271 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N SER A 444 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL A 467 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP A 446 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU A 465 " --> pdb=" O ASP A 446 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR A 448 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP A 463 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL A 450 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 459 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ILE A 459 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N GLN A 306 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA A 461 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 465 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 355 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.629A pdb=" N ARG B 51 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TYR B 171 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE B 53 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N MET B 173 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE B 166 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP B 154 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 172 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 93 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LYS B 101 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU B 80 " --> pdb=" O LYS B 101 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 704 1.31 - 1.44: 1113 1.44 - 1.57: 2426 1.57 - 1.70: 0 1.70 - 1.83: 32 Bond restraints: 4275 Sorted by residual: bond pdb=" CA SER A 441 " pdb=" CB SER A 441 " ideal model delta sigma weight residual 1.531 1.443 0.089 1.67e-02 3.59e+03 2.81e+01 bond pdb=" N CYS B 50 " pdb=" CA CYS B 50 " ideal model delta sigma weight residual 1.455 1.512 -0.057 1.25e-02 6.40e+03 2.08e+01 bond pdb=" C PRO A 379 " pdb=" O PRO A 379 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.30e-02 5.92e+03 1.77e+01 bond pdb=" CA ALA B 79 " pdb=" CB ALA B 79 " ideal model delta sigma weight residual 1.530 1.461 0.069 1.69e-02 3.50e+03 1.68e+01 bond pdb=" N PRO A 379 " pdb=" CA PRO A 379 " ideal model delta sigma weight residual 1.469 1.417 0.052 1.28e-02 6.10e+03 1.62e+01 ... (remaining 4270 not shown) Histogram of bond angle deviations from ideal: 93.14 - 101.53: 19 101.53 - 109.92: 645 109.92 - 118.30: 2703 118.30 - 126.69: 2376 126.69 - 135.08: 58 Bond angle restraints: 5801 Sorted by residual: angle pdb=" N PRO A 379 " pdb=" CA PRO A 379 " pdb=" CB PRO A 379 " ideal model delta sigma weight residual 103.25 93.14 10.11 1.05e+00 9.07e-01 9.27e+01 angle pdb=" C ARG A 217 " pdb=" CA ARG A 217 " pdb=" CB ARG A 217 " ideal model delta sigma weight residual 110.35 96.75 13.60 1.78e+00 3.16e-01 5.83e+01 angle pdb=" C ILE B 52 " pdb=" N ILE B 53 " pdb=" CA ILE B 53 " ideal model delta sigma weight residual 121.97 135.08 -13.11 1.80e+00 3.09e-01 5.30e+01 angle pdb=" C ASN A 437 " pdb=" CA ASN A 437 " pdb=" CB ASN A 437 " ideal model delta sigma weight residual 110.42 98.43 11.99 1.99e+00 2.53e-01 3.63e+01 angle pdb=" CA PHE A 270 " pdb=" CB PHE A 270 " pdb=" CG PHE A 270 " ideal model delta sigma weight residual 113.80 119.77 -5.97 1.00e+00 1.00e+00 3.56e+01 ... (remaining 5796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 2154 16.50 - 33.00: 287 33.00 - 49.49: 113 49.49 - 65.99: 27 65.99 - 82.49: 8 Dihedral angle restraints: 2589 sinusoidal: 1012 harmonic: 1577 Sorted by residual: dihedral pdb=" C ARG A 217 " pdb=" N ARG A 217 " pdb=" CA ARG A 217 " pdb=" CB ARG A 217 " ideal model delta harmonic sigma weight residual -122.60 -103.86 -18.74 0 2.50e+00 1.60e-01 5.62e+01 dihedral pdb=" N PRO A 379 " pdb=" C PRO A 379 " pdb=" CA PRO A 379 " pdb=" CB PRO A 379 " ideal model delta harmonic sigma weight residual 115.10 98.73 16.37 0 2.50e+00 1.60e-01 4.29e+01 dihedral pdb=" C PRO A 379 " pdb=" N PRO A 379 " pdb=" CA PRO A 379 " pdb=" CB PRO A 379 " ideal model delta harmonic sigma weight residual -120.70 -104.40 -16.30 0 2.50e+00 1.60e-01 4.25e+01 ... (remaining 2586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 573 0.081 - 0.162: 70 0.162 - 0.243: 17 0.243 - 0.325: 4 0.325 - 0.406: 1 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA ARG A 217 " pdb=" N ARG A 217 " pdb=" C ARG A 217 " pdb=" CB ARG A 217 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA ASP B 34 " pdb=" N ASP B 34 " pdb=" C ASP B 34 " pdb=" CB ASP B 34 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ASN A 189 " pdb=" N ASN A 189 " pdb=" C ASN A 189 " pdb=" CB ASN A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 662 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 79 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ALA B 79 " 0.066 2.00e-02 2.50e+03 pdb=" O ALA B 79 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU B 80 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 252 " 0.020 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ARG A 252 " -0.066 2.00e-02 2.50e+03 pdb=" O ARG A 252 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A 253 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 265 " 0.017 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C MET A 265 " -0.063 2.00e-02 2.50e+03 pdb=" O MET A 265 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS A 266 " 0.021 2.00e-02 2.50e+03 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1073 2.78 - 3.31: 3966 3.31 - 3.84: 6284 3.84 - 4.37: 7294 4.37 - 4.90: 12513 Nonbonded interactions: 31130 Sorted by model distance: nonbonded pdb=" O GLY A 278 " pdb=" OG SER A 281 " model vdw 2.254 2.440 nonbonded pdb=" O ASP A 102 " pdb=" OG SER A 105 " model vdw 2.315 2.440 nonbonded pdb=" CB ASN A 437 " pdb=" N ASN A 438 " model vdw 2.325 2.816 nonbonded pdb=" O GLN A 255 " pdb=" C LYS A 256 " model vdw 2.328 3.270 nonbonded pdb=" O LEU A 257 " pdb=" N THR A 259 " model vdw 2.331 2.520 ... (remaining 31125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.550 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.780 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.007 0.089 4275 Z= 0.455 Angle : 1.240 13.597 5801 Z= 0.781 Chirality : 0.063 0.406 665 Planarity : 0.007 0.090 748 Dihedral : 18.565 82.489 1559 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 2.65 % Allowed : 7.39 % Favored : 89.96 % Rotamer: Outliers : 6.10 % Allowed : 28.10 % Favored : 65.80 % Cbeta Deviations : 0.97 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.36), residues: 528 helix: -1.59 (0.46), residues: 118 sheet: -0.36 (0.59), residues: 98 loop : -1.12 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 209 HIS 0.004 0.001 HIS B 86 PHE 0.023 0.002 PHE A 270 TYR 0.021 0.002 TYR A 382 ARG 0.006 0.001 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8332 (mmt) REVERT: A 379 PRO cc_start: 0.9471 (OUTLIER) cc_final: 0.8857 (Cg_exo) REVERT: B 32 ASP cc_start: 0.8854 (t0) cc_final: 0.8620 (t0) REVERT: B 134 MET cc_start: 0.7455 (ptt) cc_final: 0.6901 (tpt) REVERT: B 167 SER cc_start: 0.8630 (p) cc_final: 0.8350 (p) outliers start: 28 outliers final: 9 residues processed: 122 average time/residue: 0.1341 time to fit residues: 20.3554 Evaluate side-chains 80 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 379 PRO Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 34 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 224 ASN A 380 ASN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN B 61 GLN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4275 Z= 0.233 Angle : 0.717 6.665 5801 Z= 0.369 Chirality : 0.047 0.192 665 Planarity : 0.005 0.065 748 Dihedral : 8.566 68.634 596 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.95 % Allowed : 5.68 % Favored : 93.37 % Rotamer: Outliers : 8.71 % Allowed : 27.89 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.37), residues: 528 helix: -0.88 (0.45), residues: 137 sheet: -0.49 (0.51), residues: 111 loop : -0.64 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 292 HIS 0.003 0.001 HIS A 400 PHE 0.010 0.001 PHE A 395 TYR 0.014 0.002 TYR B 85 ARG 0.002 0.001 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 66 time to evaluate : 0.510 Fit side-chains REVERT: A 124 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8884 (tt) REVERT: A 255 GLN cc_start: 0.9419 (OUTLIER) cc_final: 0.9124 (pp30) REVERT: A 302 LEU cc_start: 0.9132 (mt) cc_final: 0.8900 (mp) REVERT: A 335 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8268 (mmt) REVERT: B 32 ASP cc_start: 0.8778 (t0) cc_final: 0.8521 (t0) REVERT: B 134 MET cc_start: 0.7461 (ptt) cc_final: 0.6896 (tpt) outliers start: 40 outliers final: 20 residues processed: 95 average time/residue: 0.1369 time to fit residues: 17.1727 Evaluate side-chains 81 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 179 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 437 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4275 Z= 0.206 Angle : 0.648 7.443 5801 Z= 0.329 Chirality : 0.045 0.196 665 Planarity : 0.004 0.054 748 Dihedral : 7.129 67.841 579 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.68 % Favored : 93.75 % Rotamer: Outliers : 6.54 % Allowed : 27.02 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.38), residues: 528 helix: -0.02 (0.48), residues: 131 sheet: -0.16 (0.51), residues: 106 loop : -0.40 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 292 HIS 0.002 0.001 HIS A 373 PHE 0.015 0.001 PHE A 106 TYR 0.012 0.001 TYR A 382 ARG 0.002 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 55 time to evaluate : 0.509 Fit side-chains REVERT: A 124 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8977 (tt) REVERT: A 335 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8573 (mmm) REVERT: A 374 HIS cc_start: 0.7574 (m-70) cc_final: 0.7373 (m-70) REVERT: A 398 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8786 (p) REVERT: B 134 MET cc_start: 0.7466 (ptt) cc_final: 0.6908 (tpt) outliers start: 30 outliers final: 20 residues processed: 78 average time/residue: 0.1368 time to fit residues: 14.3387 Evaluate side-chains 72 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 49 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 48 optimal weight: 0.0000 chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4275 Z= 0.176 Angle : 0.605 6.554 5801 Z= 0.305 Chirality : 0.045 0.170 665 Planarity : 0.004 0.049 748 Dihedral : 6.189 59.612 576 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.87 % Favored : 93.75 % Rotamer: Outliers : 6.10 % Allowed : 26.58 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.37), residues: 528 helix: 0.13 (0.48), residues: 132 sheet: -0.21 (0.53), residues: 98 loop : -0.48 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 292 HIS 0.002 0.001 HIS A 373 PHE 0.024 0.001 PHE A 106 TYR 0.017 0.001 TYR B 85 ARG 0.002 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 52 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9072 (tt) REVERT: B 134 MET cc_start: 0.7469 (ptt) cc_final: 0.6911 (tpt) REVERT: B 182 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9102 (mm) outliers start: 28 outliers final: 20 residues processed: 73 average time/residue: 0.1262 time to fit residues: 12.5983 Evaluate side-chains 67 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 182 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4275 Z= 0.176 Angle : 0.628 6.790 5801 Z= 0.309 Chirality : 0.044 0.160 665 Planarity : 0.003 0.045 748 Dihedral : 5.722 56.653 572 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.87 % Favored : 93.75 % Rotamer: Outliers : 5.45 % Allowed : 28.76 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.37), residues: 528 helix: -0.05 (0.46), residues: 128 sheet: -0.10 (0.53), residues: 98 loop : -0.51 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 292 HIS 0.006 0.001 HIS A 374 PHE 0.017 0.001 PHE A 106 TYR 0.011 0.001 TYR A 428 ARG 0.002 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 56 time to evaluate : 0.521 Fit side-chains REVERT: B 106 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8659 (mp0) REVERT: B 134 MET cc_start: 0.7269 (ptt) cc_final: 0.6571 (tpt) outliers start: 25 outliers final: 20 residues processed: 74 average time/residue: 0.1272 time to fit residues: 12.7514 Evaluate side-chains 72 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 155 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.0040 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN B 29 HIS ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4275 Z= 0.190 Angle : 0.625 9.301 5801 Z= 0.302 Chirality : 0.043 0.156 665 Planarity : 0.003 0.042 748 Dihedral : 5.646 54.652 572 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.44 % Favored : 93.18 % Rotamer: Outliers : 5.23 % Allowed : 27.67 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.37), residues: 528 helix: -0.14 (0.45), residues: 134 sheet: -0.05 (0.52), residues: 97 loop : -0.58 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 292 HIS 0.004 0.001 HIS B 86 PHE 0.019 0.001 PHE A 106 TYR 0.011 0.001 TYR A 428 ARG 0.002 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 54 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9080 (tt) REVERT: B 134 MET cc_start: 0.7292 (ptt) cc_final: 0.6578 (tpt) outliers start: 24 outliers final: 20 residues processed: 71 average time/residue: 0.1342 time to fit residues: 12.8591 Evaluate side-chains 70 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 49 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 182 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 0.0060 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4275 Z= 0.193 Angle : 0.627 8.220 5801 Z= 0.304 Chirality : 0.043 0.154 665 Planarity : 0.003 0.041 748 Dihedral : 5.576 54.342 572 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.25 % Favored : 93.37 % Rotamer: Outliers : 5.45 % Allowed : 28.10 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.36), residues: 528 helix: -0.17 (0.45), residues: 134 sheet: -0.17 (0.51), residues: 96 loop : -0.62 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 449 HIS 0.003 0.001 HIS A 373 PHE 0.015 0.001 PHE A 106 TYR 0.010 0.001 TYR A 428 ARG 0.005 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 51 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.8867 (mmm) cc_final: 0.8581 (mmt) REVERT: B 106 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8553 (mp0) REVERT: B 134 MET cc_start: 0.7311 (ptt) cc_final: 0.6578 (tpt) outliers start: 25 outliers final: 21 residues processed: 69 average time/residue: 0.1307 time to fit residues: 12.1734 Evaluate side-chains 68 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 47 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 182 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.0670 chunk 25 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.0270 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4275 Z= 0.163 Angle : 0.635 7.905 5801 Z= 0.302 Chirality : 0.043 0.152 665 Planarity : 0.003 0.039 748 Dihedral : 5.416 52.082 572 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.49 % Favored : 94.13 % Rotamer: Outliers : 4.14 % Allowed : 30.07 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.36), residues: 528 helix: 0.02 (0.48), residues: 122 sheet: -0.00 (0.50), residues: 96 loop : -0.54 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 292 HIS 0.004 0.001 HIS B 86 PHE 0.016 0.001 PHE A 106 TYR 0.011 0.001 TYR A 428 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.8857 (mmm) cc_final: 0.8615 (mmt) REVERT: B 106 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8503 (mp0) REVERT: B 134 MET cc_start: 0.7297 (ptt) cc_final: 0.6579 (tpt) REVERT: B 183 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8777 (mmmt) outliers start: 19 outliers final: 18 residues processed: 68 average time/residue: 0.1342 time to fit residues: 12.3502 Evaluate side-chains 72 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 47 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.0050 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4275 Z= 0.160 Angle : 0.659 11.827 5801 Z= 0.304 Chirality : 0.043 0.154 665 Planarity : 0.003 0.038 748 Dihedral : 5.267 49.883 572 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.87 % Favored : 93.75 % Rotamer: Outliers : 3.70 % Allowed : 31.15 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.37), residues: 528 helix: 0.05 (0.49), residues: 122 sheet: 0.06 (0.50), residues: 96 loop : -0.51 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 292 HIS 0.003 0.001 HIS B 86 PHE 0.016 0.001 PHE A 106 TYR 0.011 0.001 TYR B 171 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.8868 (mmm) cc_final: 0.8666 (mmt) REVERT: B 106 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8473 (mp0) REVERT: B 134 MET cc_start: 0.7306 (ptt) cc_final: 0.6585 (tpt) outliers start: 17 outliers final: 16 residues processed: 72 average time/residue: 0.1236 time to fit residues: 11.9819 Evaluate side-chains 70 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4275 Z= 0.204 Angle : 0.699 12.075 5801 Z= 0.323 Chirality : 0.043 0.155 665 Planarity : 0.003 0.038 748 Dihedral : 5.327 51.263 572 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.87 % Favored : 93.75 % Rotamer: Outliers : 4.14 % Allowed : 31.59 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.37), residues: 528 helix: 0.10 (0.48), residues: 122 sheet: 0.04 (0.50), residues: 96 loop : -0.45 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 449 HIS 0.003 0.001 HIS B 86 PHE 0.017 0.001 PHE A 106 TYR 0.010 0.001 TYR A 428 ARG 0.002 0.000 ARG A 447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 0.511 Fit side-chains REVERT: A 335 MET cc_start: 0.8904 (mmm) cc_final: 0.8655 (mmt) REVERT: B 134 MET cc_start: 0.7345 (ptt) cc_final: 0.6592 (tpt) outliers start: 19 outliers final: 17 residues processed: 66 average time/residue: 0.1370 time to fit residues: 12.0743 Evaluate side-chains 67 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 50 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 182 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 48 optimal weight: 0.0020 chunk 28 optimal weight: 0.9980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 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 = 0.3374 r_free = 0.3374 target = 0.071192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055992 restraints weight = 18383.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.057602 restraints weight = 10760.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.058732 restraints weight = 7571.786| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4275 Z= 0.180 Angle : 0.704 11.929 5801 Z= 0.325 Chirality : 0.044 0.154 665 Planarity : 0.003 0.038 748 Dihedral : 5.425 51.854 572 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.44 % Favored : 93.37 % Rotamer: Outliers : 3.92 % Allowed : 32.03 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.37), residues: 528 helix: 0.10 (0.49), residues: 122 sheet: -0.00 (0.50), residues: 96 loop : -0.47 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 292 HIS 0.003 0.001 HIS B 86 PHE 0.016 0.001 PHE A 106 TYR 0.010 0.001 TYR A 428 ARG 0.002 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1363.28 seconds wall clock time: 26 minutes 10.72 seconds (1570.72 seconds total)