Starting phenix.real_space_refine on Mon Nov 13 18:56:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbn_34638/11_2023/8hbn_34638.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbn_34638/11_2023/8hbn_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_34638/11_2023/8hbn_34638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbn_34638/11_2023/8hbn_34638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbn_34638/11_2023/8hbn_34638.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbn_34638/11_2023/8hbn_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 3.00, per 1000 atoms: 0.72 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: 2.07 Conformation dependent library (CDL) restraints added in 784.1 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: 0.37 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: 1.15 Time building geometry restraints manager: 2.24 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: 2.720 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: 12.670 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 18.380 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: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.210 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 122 average time/residue: 0.1616 time to fit residues: 24.4965 Evaluate side-chains 78 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1273 time to fit residues: 2.0822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 22 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.0050 overall best weight: 0.4752 ------------------------------------------------------------------------------- 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: 0.8232 moved from start: 0.2651 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= 0.205 Angle : 0.729 7.383 5801 Z= 0.376 Chirality : 0.048 0.168 665 Planarity : 0.006 0.087 748 Dihedral : 4.886 29.078 567 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.95 % Allowed : 5.87 % Favored : 93.18 % Rotamer: Outliers : 6.54 % Allowed : 27.45 % Favored : 66.01 % 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: -1.03 (0.37), residues: 528 helix: -0.85 (0.45), residues: 136 sheet: -0.41 (0.50), residues: 116 loop : -0.60 (0.38), residues: 276 *********************** 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 101 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 71 time to evaluate : 0.509 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 93 average time/residue: 0.1371 time to fit residues: 16.9906 Evaluate side-chains 81 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0733 time to fit residues: 2.3551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** 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: 0.8318 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4275 Z= 0.287 Angle : 0.681 8.094 5801 Z= 0.348 Chirality : 0.045 0.153 665 Planarity : 0.005 0.052 748 Dihedral : 4.919 25.538 567 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.49 % Favored : 93.75 % Rotamer: Outliers : 2.61 % Allowed : 28.76 % Favored : 68.63 % 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 (0.38), residues: 528 helix: -0.10 (0.48), residues: 124 sheet: -0.35 (0.50), residues: 106 loop : -0.34 (0.39), residues: 298 *********************** 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 67 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.527 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.1323 time to fit residues: 11.6224 Evaluate side-chains 58 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0495 time to fit residues: 1.2935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4275 Z= 0.182 Angle : 0.627 9.100 5801 Z= 0.315 Chirality : 0.045 0.159 665 Planarity : 0.004 0.047 748 Dihedral : 4.561 21.270 567 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.87 % Favored : 93.75 % Rotamer: Outliers : 3.27 % Allowed : 27.89 % Favored : 68.85 % 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: -0.62 (0.37), residues: 528 helix: -0.17 (0.48), residues: 128 sheet: -0.36 (0.52), residues: 97 loop : -0.45 (0.37), residues: 303 *********************** 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 69 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.510 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 64 average time/residue: 0.1360 time to fit residues: 11.8623 Evaluate side-chains 57 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.545 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0463 time to fit residues: 1.3412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN A 380 ASN B 29 HIS ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4275 Z= 0.256 Angle : 0.653 9.885 5801 Z= 0.327 Chirality : 0.044 0.147 665 Planarity : 0.004 0.045 748 Dihedral : 4.632 20.950 567 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.82 % Favored : 92.80 % Rotamer: Outliers : 1.74 % Allowed : 30.07 % Favored : 68.19 % 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: -0.79 (0.37), residues: 528 helix: -0.37 (0.46), residues: 134 sheet: -0.67 (0.49), residues: 99 loop : -0.44 (0.38), residues: 295 *********************** 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 56 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.451 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 55 average time/residue: 0.1310 time to fit residues: 9.8414 Evaluate side-chains 46 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0538 time to fit residues: 0.9957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8384 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4275 Z= 0.268 Angle : 0.667 10.479 5801 Z= 0.329 Chirality : 0.044 0.148 665 Planarity : 0.004 0.044 748 Dihedral : 4.693 21.092 567 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.39 % Favored : 92.23 % Rotamer: Outliers : 1.09 % Allowed : 30.28 % Favored : 68.63 % 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: -0.80 (0.37), residues: 528 helix: -0.38 (0.46), residues: 134 sheet: -0.61 (0.49), residues: 97 loop : -0.48 (0.38), residues: 297 *********************** 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 50 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.1409 time to fit residues: 9.0812 Evaluate side-chains 47 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0453 time to fit residues: 0.9547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.8388 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4275 Z= 0.235 Angle : 0.646 10.352 5801 Z= 0.318 Chirality : 0.044 0.146 665 Planarity : 0.004 0.044 748 Dihedral : 4.605 20.996 567 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.01 % Favored : 92.61 % Rotamer: Outliers : 1.53 % Allowed : 30.94 % Favored : 67.54 % 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: -0.86 (0.37), residues: 528 helix: -0.39 (0.46), residues: 134 sheet: -0.75 (0.48), residues: 99 loop : -0.49 (0.38), residues: 295 *********************** 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 55 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.497 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 0.1333 time to fit residues: 9.9166 Evaluate side-chains 47 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0468 time to fit residues: 1.0041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5061 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= 0.190 Angle : 0.673 11.043 5801 Z= 0.322 Chirality : 0.044 0.149 665 Planarity : 0.004 0.041 748 Dihedral : 4.487 20.876 567 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.44 % Favored : 93.18 % Rotamer: Outliers : 0.44 % Allowed : 31.15 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.37), residues: 528 helix: -0.33 (0.47), residues: 134 sheet: -0.56 (0.49), residues: 99 loop : -0.54 (0.38), residues: 295 *********************** 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 49 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.519 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.1383 time to fit residues: 8.9089 Evaluate side-chains 43 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.482 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0508 time to fit residues: 0.8778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.0170 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5175 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= 0.192 Angle : 0.727 12.828 5801 Z= 0.339 Chirality : 0.044 0.149 665 Planarity : 0.004 0.041 748 Dihedral : 4.454 20.590 567 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.82 % Favored : 92.80 % Rotamer: Outliers : 0.44 % Allowed : 33.12 % 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: -0.80 (0.37), residues: 528 helix: -0.26 (0.47), residues: 132 sheet: -0.52 (0.49), residues: 99 loop : -0.57 (0.38), residues: 297 *********************** 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 48 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.517 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.1432 time to fit residues: 9.1824 Evaluate side-chains 46 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.495 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0463 time to fit residues: 0.7990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 0.0370 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5292 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= 0.205 Angle : 0.737 12.504 5801 Z= 0.351 Chirality : 0.045 0.209 665 Planarity : 0.004 0.041 748 Dihedral : 4.460 20.251 567 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.01 % Favored : 92.61 % Rotamer: Outliers : 0.44 % Allowed : 32.90 % Favored : 66.67 % 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: -0.76 (0.37), residues: 528 helix: -0.18 (0.48), residues: 132 sheet: -0.51 (0.49), residues: 99 loop : -0.57 (0.38), residues: 297 ********************** 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 44 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.514 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 42 average time/residue: 0.1487 time to fit residues: 8.5189 Evaluate side-chains 44 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0554 time to fit residues: 0.8417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 chunk 48 optimal weight: 0.0670 chunk 28 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3367 r_free = 0.3367 target = 0.070150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055321 restraints weight = 18169.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.056934 restraints weight = 10580.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058048 restraints weight = 7406.216| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4275 Z= 0.185 Angle : 0.727 11.991 5801 Z= 0.344 Chirality : 0.045 0.204 665 Planarity : 0.003 0.040 748 Dihedral : 4.344 20.664 567 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.20 % Favored : 92.42 % Rotamer: Outliers : 1.09 % Allowed : 32.24 % Favored : 66.67 % 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: -0.67 (0.37), residues: 528 helix: -0.09 (0.48), residues: 132 sheet: -0.41 (0.49), residues: 99 loop : -0.54 (0.38), residues: 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.04 seconds wall clock time: 27 minutes 49.98 seconds (1669.98 seconds total)