Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 08:20:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/04_2023/7p1j_13162.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/04_2023/7p1j_13162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/04_2023/7p1j_13162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/04_2023/7p1j_13162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/04_2023/7p1j_13162.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1j_13162/04_2023/7p1j_13162.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 38 5.16 5 C 4334 2.51 5 N 1034 2.21 5 O 1096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6502 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3251 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain breaks: 1 Chain: "A" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3251 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain breaks: 1 Time building chain proxies: 3.94, per 1000 atoms: 0.61 Number of scatterers: 6502 At special positions: 0 Unit cell: (119.312, 90.2625, 85.075, 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 38 16.00 O 1096 8.00 N 1034 7.00 C 4334 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: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 80 through 104 removed outlier: 4.203A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 removed outlier: 4.216A pdb=" N GLY B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 4.490A pdb=" N GLY B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 168 through 190 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 200 through 223 Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 244 through 259 removed outlier: 4.147A pdb=" N VAL B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 276 through 293 removed outlier: 4.057A pdb=" N LEU B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 321 removed outlier: 3.664A pdb=" N PHE B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 357 Processing helix chain 'B' and resid 360 through 377 removed outlier: 3.966A pdb=" N LEU B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 367 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 404 removed outlier: 3.561A pdb=" N LYS B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Proline residue: B 397 - end of helix Processing helix chain 'B' and resid 417 through 439 Processing helix chain 'B' and resid 446 through 455 removed outlier: 3.888A pdb=" N ILE B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 478 removed outlier: 4.214A pdb=" N ALA B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 516 removed outlier: 3.529A pdb=" N ALA B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Proline residue: B 502 - end of helix Proline residue: B 513 - end of helix removed outlier: 3.714A pdb=" N LEU B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 105 removed outlier: 4.099A pdb=" N VAL A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 134 removed outlier: 4.207A pdb=" N GLY A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 4.392A pdb=" N GLY A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.961A pdb=" N ASN A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 191 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 200 through 223 Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 229 through 241 Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.688A pdb=" N VAL A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Proline residue: A 250 - end of helix removed outlier: 3.550A pdb=" N GLY A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 293 removed outlier: 4.238A pdb=" N SER A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 removed outlier: 3.806A pdb=" N PHE A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 357 removed outlier: 3.501A pdb=" N PHE A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 377 removed outlier: 4.015A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 4.250A pdb=" N VAL A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 417 through 439 removed outlier: 3.527A pdb=" N VAL A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 455 removed outlier: 3.942A pdb=" N ILE A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 removed outlier: 4.000A pdb=" N ALA A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 516 removed outlier: 3.614A pdb=" N ALA A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Proline residue: A 502 - end of helix Proline residue: A 513 - end of helix removed outlier: 3.704A pdb=" N LEU A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1488 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: 1.86 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1966 1.34 - 1.46: 1378 1.46 - 1.58: 3244 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6646 Sorted by residual: bond pdb=" N VAL B 158 " pdb=" CA VAL B 158 " ideal model delta sigma weight residual 1.454 1.461 -0.007 7.70e-03 1.69e+04 8.11e-01 bond pdb=" C TYR A 325 " pdb=" N PHE A 326 " ideal model delta sigma weight residual 1.332 1.344 -0.011 1.50e-02 4.44e+03 5.57e-01 bond pdb=" CA LEU A 208 " pdb=" C LEU A 208 " ideal model delta sigma weight residual 1.519 1.527 -0.008 1.22e-02 6.72e+03 4.58e-01 bond pdb=" C PHE A 326 " pdb=" N PRO A 327 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 4.04e-01 bond pdb=" N VAL A 158 " pdb=" CA VAL A 158 " ideal model delta sigma weight residual 1.461 1.454 0.007 1.23e-02 6.61e+03 3.42e-01 ... (remaining 6641 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 208 107.13 - 113.85: 3910 113.85 - 120.57: 2642 120.57 - 127.29: 2214 127.29 - 134.01: 78 Bond angle restraints: 9052 Sorted by residual: angle pdb=" C VAL A 248 " pdb=" N VAL A 249 " pdb=" CA VAL A 249 " ideal model delta sigma weight residual 120.33 122.82 -2.49 8.00e-01 1.56e+00 9.68e+00 angle pdb=" CA LEU B 412 " pdb=" CB LEU B 412 " pdb=" CG LEU B 412 " ideal model delta sigma weight residual 116.30 124.96 -8.66 3.50e+00 8.16e-02 6.13e+00 angle pdb=" CA LEU A 412 " pdb=" CB LEU A 412 " pdb=" CG LEU A 412 " ideal model delta sigma weight residual 116.30 124.94 -8.64 3.50e+00 8.16e-02 6.09e+00 angle pdb=" C ALA A 460 " pdb=" N THR A 461 " pdb=" CA THR A 461 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.91e+00 angle pdb=" C VAL A 249 " pdb=" CA VAL A 249 " pdb=" CB VAL A 249 " ideal model delta sigma weight residual 114.00 111.22 2.78 1.31e+00 5.83e-01 4.51e+00 ... (remaining 9047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.46: 3577 11.46 - 22.92: 186 22.92 - 34.38: 62 34.38 - 45.84: 28 45.84 - 57.30: 5 Dihedral angle restraints: 3858 sinusoidal: 1436 harmonic: 2422 Sorted by residual: dihedral pdb=" N ARG A 176 " pdb=" CA ARG A 176 " pdb=" CB ARG A 176 " pdb=" CG ARG A 176 " ideal model delta sinusoidal sigma weight residual -60.00 -117.30 57.30 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N PHE A 356 " pdb=" CA PHE A 356 " pdb=" CB PHE A 356 " pdb=" CG PHE A 356 " ideal model delta sinusoidal sigma weight residual -180.00 -127.72 -52.28 3 1.50e+01 4.44e-03 9.10e+00 dihedral pdb=" N TRP A 171 " pdb=" CA TRP A 171 " pdb=" CB TRP A 171 " pdb=" CG TRP A 171 " ideal model delta sinusoidal sigma weight residual -60.00 -108.02 48.02 3 1.50e+01 4.44e-03 8.58e+00 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 661 0.023 - 0.045: 245 0.045 - 0.068: 152 0.068 - 0.090: 35 0.090 - 0.113: 25 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CA ILE B 167 " pdb=" N ILE B 167 " pdb=" C ILE B 167 " pdb=" CB ILE B 167 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CG LEU A 412 " pdb=" CB LEU A 412 " pdb=" CD1 LEU A 412 " pdb=" CD2 LEU A 412 " both_signs ideal model delta sigma weight residual False -2.59 -2.48 -0.11 2.00e-01 2.50e+01 3.11e-01 chirality pdb=" CA PRO B 210 " pdb=" N PRO B 210 " pdb=" C PRO B 210 " pdb=" CB PRO B 210 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.01e-01 ... (remaining 1115 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 512 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A 513 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 513 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 109 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 110 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 512 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 513 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 513 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 513 " -0.017 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1902 2.82 - 3.34: 6870 3.34 - 3.86: 10382 3.86 - 4.38: 10917 4.38 - 4.90: 19952 Nonbonded interactions: 50023 Sorted by model distance: nonbonded pdb=" O PHE A 153 " pdb=" ND2 ASN A 157 " model vdw 2.305 2.520 nonbonded pdb=" O PHE A 444 " pdb=" NZ LYS A 449 " model vdw 2.314 2.520 nonbonded pdb=" O PHE B 444 " pdb=" NZ LYS B 449 " model vdw 2.315 2.520 nonbonded pdb=" OG SER B 106 " pdb=" OE1 GLU B 107 " model vdw 2.322 2.440 nonbonded pdb=" O PHE B 153 " pdb=" ND2 ASN B 157 " model vdw 2.372 2.520 ... (remaining 50018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 3.400 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.420 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 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 : 0.002 0.018 6646 Z= 0.104 Angle : 0.476 8.663 9052 Z= 0.238 Chirality : 0.034 0.113 1118 Planarity : 0.003 0.042 1094 Dihedral : 8.895 57.299 2314 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 2.29 % 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: 2.14 (0.30), residues: 860 helix: 2.30 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.03 (0.49), residues: 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 231 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 242 average time/residue: 0.1569 time to fit residues: 51.9939 Evaluate side-chains 129 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0864 time to fit residues: 1.5067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 6646 Z= 0.243 Angle : 0.804 11.608 9052 Z= 0.380 Chirality : 0.045 0.385 1118 Planarity : 0.005 0.076 1094 Dihedral : 3.544 17.399 902 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 4.58 % 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: 1.89 (0.30), residues: 860 helix: 2.15 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -2.32 (0.48), residues: 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 22 residues processed: 165 average time/residue: 0.1376 time to fit residues: 32.4733 Evaluate side-chains 138 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0705 time to fit residues: 3.6952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 84 optimal weight: 0.0980 chunk 69 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6646 Z= 0.189 Angle : 0.767 12.578 9052 Z= 0.353 Chirality : 0.043 0.276 1118 Planarity : 0.004 0.037 1094 Dihedral : 3.835 20.512 902 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 3.15 % 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: 1.58 (0.30), residues: 860 helix: 1.96 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.38 (0.45), residues: 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 2 residues processed: 143 average time/residue: 0.1299 time to fit residues: 26.9215 Evaluate side-chains 122 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0721 time to fit residues: 1.2748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 6646 Z= 0.330 Angle : 0.813 11.178 9052 Z= 0.391 Chirality : 0.044 0.310 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.117 21.195 902 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 4.87 % 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: 0.98 (0.29), residues: 860 helix: 1.54 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.60 (0.44), residues: 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 141 average time/residue: 0.1352 time to fit residues: 27.3070 Evaluate side-chains 123 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0609 time to fit residues: 3.0171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 6646 Z= 0.191 Angle : 0.787 14.126 9052 Z= 0.360 Chirality : 0.042 0.343 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.066 18.876 902 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 2.01 % 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: 0.94 (0.29), residues: 860 helix: 1.54 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -2.68 (0.44), residues: 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 121 average time/residue: 0.1364 time to fit residues: 23.9532 Evaluate side-chains 105 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0591 time to fit residues: 1.5325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 43 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 6646 Z= 0.190 Angle : 0.779 14.027 9052 Z= 0.359 Chirality : 0.043 0.516 1118 Planarity : 0.004 0.040 1094 Dihedral : 4.009 17.488 902 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer Outliers : 1.43 % 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: 1.01 (0.30), residues: 860 helix: 1.62 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -2.74 (0.44), residues: 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 117 average time/residue: 0.1360 time to fit residues: 23.2531 Evaluate side-chains 108 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0696 time to fit residues: 1.5551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6646 Z= 0.226 Angle : 0.796 13.939 9052 Z= 0.373 Chirality : 0.045 0.454 1118 Planarity : 0.004 0.042 1094 Dihedral : 4.076 18.633 902 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer Outliers : 2.15 % 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 (0.29), residues: 860 helix: 1.47 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -2.69 (0.45), residues: 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.755 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 110 average time/residue: 0.1389 time to fit residues: 22.2672 Evaluate side-chains 101 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0607 time to fit residues: 1.5718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6646 Z= 0.190 Angle : 0.782 14.192 9052 Z= 0.362 Chirality : 0.043 0.320 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.036 17.649 902 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 1.15 % 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: 0.85 (0.29), residues: 860 helix: 1.48 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -2.74 (0.44), residues: 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.756 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 108 average time/residue: 0.1414 time to fit residues: 22.0976 Evaluate side-chains 103 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1207 time to fit residues: 2.1685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 76 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6646 Z= 0.203 Angle : 0.814 14.323 9052 Z= 0.379 Chirality : 0.044 0.272 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.062 17.605 902 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 0.57 % 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: 0.74 (0.29), residues: 860 helix: 1.41 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -2.73 (0.44), residues: 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.701 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 109 average time/residue: 0.1353 time to fit residues: 21.6178 Evaluate side-chains 98 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0619 time to fit residues: 1.1124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 54 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6646 Z= 0.202 Angle : 0.832 14.317 9052 Z= 0.385 Chirality : 0.044 0.263 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.117 17.141 902 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 0.43 % 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 (0.29), residues: 860 helix: 1.48 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -2.83 (0.42), residues: 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.806 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 102 average time/residue: 0.1407 time to fit residues: 20.9794 Evaluate side-chains 101 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.744 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0568 time to fit residues: 1.1693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 70 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 0.0010 chunk 59 optimal weight: 0.0020 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** 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 = 0.4199 r_free = 0.4199 target = 0.097751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.083671 restraints weight = 30983.752| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 4.15 r_work: 0.3788 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6646 Z= 0.179 Angle : 0.830 15.744 9052 Z= 0.383 Chirality : 0.044 0.267 1118 Planarity : 0.004 0.040 1094 Dihedral : 4.061 15.343 902 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 0.72 % 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: 0.73 (0.29), residues: 860 helix: 1.41 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -2.77 (0.43), residues: 198 =============================================================================== Job complete usr+sys time: 1629.75 seconds wall clock time: 29 minutes 56.70 seconds (1796.70 seconds total)