Starting phenix.real_space_refine (version: dev) on Sun Dec 11 18:57:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/12_2022/7p1i_13161.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/12_2022/7p1i_13161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/12_2022/7p1i_13161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/12_2022/7p1i_13161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/12_2022/7p1i_13161.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1i_13161/12_2022/7p1i_13161.pdb" } resolution = 3.15 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= 0.006 sd= 0.045 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 6644 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3322 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 21, 'TRANS': 420} Chain breaks: 1 Chain: "A" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3322 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 21, 'TRANS': 420} Chain breaks: 1 Time building chain proxies: 4.45, per 1000 atoms: 0.67 Number of scatterers: 6644 At special positions: 0 Unit cell: (121.388, 102.713, 88.1875, 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 40 16.00 O 1114 8.00 N 1074 7.00 C 4416 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: 2.88 Conformation dependent library (CDL) restraints added in 1.2 seconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 83.4% 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 70 through 77 Processing helix chain 'B' and resid 80 through 104 removed outlier: 4.409A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 removed outlier: 3.629A pdb=" N GLY B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 4.199A 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 191 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 248 through 259 Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 276 through 293 removed outlier: 4.206A pdb=" N LEU B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 326 removed outlier: 3.788A pdb=" N PHE B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 357 removed outlier: 3.541A pdb=" N GLY B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 376 removed outlier: 3.893A pdb=" N LEU B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 367 " --> pdb=" O GLY B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 405 removed outlier: 4.284A 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 416 through 439 removed outlier: 4.468A pdb=" N CYS B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 456 Processing helix chain 'B' and resid 460 through 478 removed outlier: 4.045A pdb=" N ALA B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N HIS B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 516 removed outlier: 3.603A 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: 3.819A pdb=" N LEU B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 80 through 104 removed outlier: 4.410A pdb=" N VAL A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 134 removed outlier: 3.629A pdb=" N GLY A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 4.199A pdb=" N GLY A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 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 248 through 259 Processing helix chain 'A' and resid 265 through 274 Processing helix chain 'A' and resid 276 through 293 removed outlier: 4.205A pdb=" N LEU A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 326 removed outlier: 3.787A pdb=" N PHE A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 357 removed outlier: 3.541A pdb=" N GLY A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 376 removed outlier: 3.892A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 4.285A 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 416 through 439 removed outlier: 4.468A pdb=" N CYS A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 460 through 478 removed outlier: 4.045A pdb=" N ALA A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 516 removed outlier: 3.602A 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: 3.818A pdb=" N LEU A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1527 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: 2.00 Time building geometry restraints manager: 3.11 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: 2026 1.34 - 1.46: 1388 1.46 - 1.58: 3316 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6790 Sorted by residual: bond pdb=" N ILE A 323 " pdb=" CA ILE A 323 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.41e-02 5.03e+03 5.66e+00 bond pdb=" N ILE B 323 " pdb=" CA ILE B 323 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.41e-02 5.03e+03 5.46e+00 bond pdb=" N PHE B 321 " pdb=" CA PHE B 321 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.35e-02 5.49e+03 4.07e+00 bond pdb=" N PHE A 321 " pdb=" CA PHE A 321 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.35e-02 5.49e+03 4.05e+00 bond pdb=" N GLN A 324 " pdb=" CA GLN A 324 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.61e+00 ... (remaining 6785 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.10: 212 107.10 - 113.82: 3972 113.82 - 120.55: 2703 120.55 - 127.27: 2275 127.27 - 133.99: 82 Bond angle restraints: 9244 Sorted by residual: angle pdb=" C TRP B 456 " pdb=" N LEU B 457 " pdb=" CA LEU B 457 " ideal model delta sigma weight residual 120.26 125.13 -4.87 1.34e+00 5.57e-01 1.32e+01 angle pdb=" C PHE A 322 " pdb=" CA PHE A 322 " pdb=" CB PHE A 322 " ideal model delta sigma weight residual 110.56 117.20 -6.64 1.83e+00 2.99e-01 1.32e+01 angle pdb=" C PHE B 322 " pdb=" CA PHE B 322 " pdb=" CB PHE B 322 " ideal model delta sigma weight residual 110.56 117.19 -6.63 1.83e+00 2.99e-01 1.31e+01 angle pdb=" C TRP A 456 " pdb=" N LEU A 457 " pdb=" CA LEU A 457 " ideal model delta sigma weight residual 120.26 125.11 -4.85 1.34e+00 5.57e-01 1.31e+01 angle pdb=" C GLN A 324 " pdb=" CA GLN A 324 " pdb=" CB GLN A 324 " ideal model delta sigma weight residual 110.79 105.29 5.50 1.66e+00 3.63e-01 1.10e+01 ... (remaining 9239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.80: 3639 13.80 - 27.61: 207 27.61 - 41.41: 72 41.41 - 55.21: 26 55.21 - 69.02: 8 Dihedral angle restraints: 3952 sinusoidal: 1482 harmonic: 2470 Sorted by residual: dihedral pdb=" CA ILE A 499 " pdb=" C ILE A 499 " pdb=" N THR A 500 " pdb=" CA THR A 500 " ideal model delta harmonic sigma weight residual -180.00 -164.32 -15.68 0 5.00e+00 4.00e-02 9.84e+00 dihedral pdb=" CA ILE B 499 " pdb=" C ILE B 499 " pdb=" N THR B 500 " pdb=" CA THR B 500 " ideal model delta harmonic sigma weight residual -180.00 -164.35 -15.65 0 5.00e+00 4.00e-02 9.80e+00 dihedral pdb=" N ILE A 323 " pdb=" CA ILE A 323 " pdb=" CB ILE A 323 " pdb=" CG1 ILE A 323 " ideal model delta sinusoidal sigma weight residual 60.00 2.08 57.92 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 921 0.048 - 0.096: 193 0.096 - 0.143: 18 0.143 - 0.191: 0 0.191 - 0.239: 4 Chirality restraints: 1136 Sorted by residual: chirality pdb=" CA ILE A 323 " pdb=" N ILE A 323 " pdb=" C ILE A 323 " pdb=" CB ILE A 323 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE B 323 " pdb=" N ILE B 323 " pdb=" C ILE B 323 " pdb=" CB ILE B 323 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA GLN B 324 " pdb=" N GLN B 324 " pdb=" C GLN B 324 " pdb=" CB GLN B 324 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1133 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 512 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 513 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " 0.021 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 GLY B 512 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO B 513 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 513 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 513 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 136 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 137 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " -0.019 5.00e-02 4.00e+02 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1519 2.79 - 3.32: 7275 3.32 - 3.85: 11288 3.85 - 4.37: 11385 4.37 - 4.90: 20702 Nonbonded interactions: 52169 Sorted by model distance: nonbonded pdb=" O PHE A 444 " pdb=" NZ LYS A 449 " model vdw 2.265 2.520 nonbonded pdb=" O PHE B 444 " pdb=" NZ LYS B 449 " model vdw 2.265 2.520 nonbonded pdb=" OG SER A 353 " pdb=" O PHE A 358 " model vdw 2.345 2.440 nonbonded pdb=" OG SER B 353 " pdb=" O PHE B 358 " model vdw 2.345 2.440 nonbonded pdb=" NH1 ARG B 431 " pdb=" O TRP B 456 " model vdw 2.368 2.520 ... (remaining 52164 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4416 2.51 5 N 1074 2.21 5 O 1114 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.620 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: 3.390 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.050 Process input model: 22.850 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 0.034 6790 Z= 0.136 Angle : 0.567 8.510 9244 Z= 0.300 Chirality : 0.038 0.239 1136 Planarity : 0.004 0.042 1122 Dihedral : 11.178 69.016 2376 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 5.90 % 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: 3.38 (0.31), residues: 876 helix: 3.39 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.49 (0.45), residues: 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 291 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 9 residues processed: 311 average time/residue: 0.1557 time to fit residues: 65.3022 Evaluate side-chains 207 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 198 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1227 time to fit residues: 2.6039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN B 396 GLN B 481 GLN A 89 ASN A 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 6790 Z= 0.329 Angle : 0.913 14.576 9244 Z= 0.423 Chirality : 0.044 0.214 1136 Planarity : 0.005 0.038 1122 Dihedral : 4.341 20.421 924 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 6.46 % 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: 1.59 (0.29), residues: 876 helix: 2.00 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.98 (0.42), residues: 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 194 time to evaluate : 0.735 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: 46 outliers final: 31 residues processed: 222 average time/residue: 0.1496 time to fit residues: 47.9750 Evaluate side-chains 209 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.0824 time to fit residues: 5.4332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6790 Z= 0.198 Angle : 0.848 11.168 9244 Z= 0.381 Chirality : 0.043 0.184 1136 Planarity : 0.004 0.040 1122 Dihedral : 4.371 20.132 924 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 2.67 % 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: 1.43 (0.29), residues: 876 helix: 1.88 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.97 (0.42), residues: 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 208 average time/residue: 0.1348 time to fit residues: 39.7463 Evaluate side-chains 188 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 181 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0675 time to fit residues: 1.8809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6790 Z= 0.203 Angle : 0.860 12.077 9244 Z= 0.387 Chirality : 0.043 0.195 1136 Planarity : 0.004 0.044 1122 Dihedral : 4.421 20.701 924 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.97 % 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: 1.06 (0.29), residues: 876 helix: 1.60 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -3.00 (0.42), residues: 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 190 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 194 average time/residue: 0.1334 time to fit residues: 37.0772 Evaluate side-chains 185 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0640 time to fit residues: 1.8566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6790 Z= 0.208 Angle : 0.879 13.564 9244 Z= 0.398 Chirality : 0.045 0.222 1136 Planarity : 0.004 0.043 1122 Dihedral : 4.483 24.492 924 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 2.11 % 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: 876 helix: 1.58 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -3.09 (0.40), residues: 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 191 average time/residue: 0.1447 time to fit residues: 38.6962 Evaluate side-chains 183 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 177 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0600 time to fit residues: 1.6816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 6790 Z= 0.242 Angle : 0.917 13.969 9244 Z= 0.418 Chirality : 0.046 0.247 1136 Planarity : 0.004 0.043 1122 Dihedral : 4.655 26.180 924 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 3.23 % 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: 0.75 (0.29), residues: 876 helix: 1.39 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -3.02 (0.41), residues: 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 192 average time/residue: 0.1370 time to fit residues: 37.2949 Evaluate side-chains 182 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0606 time to fit residues: 2.4000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 47 optimal weight: 0.0870 chunk 84 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 0.0370 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 6790 Z= 0.205 Angle : 0.939 13.942 9244 Z= 0.418 Chirality : 0.045 0.222 1136 Planarity : 0.004 0.043 1122 Dihedral : 4.517 23.808 924 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 1.97 % 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: 0.78 (0.29), residues: 876 helix: 1.43 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -3.07 (0.40), residues: 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 190 average time/residue: 0.1385 time to fit residues: 37.4934 Evaluate side-chains 175 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0681 time to fit residues: 1.4151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.0670 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 6790 Z= 0.213 Angle : 0.967 13.786 9244 Z= 0.427 Chirality : 0.046 0.385 1136 Planarity : 0.004 0.043 1122 Dihedral : 4.511 23.211 924 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 0.98 % 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: 0.77 (0.29), residues: 876 helix: 1.41 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -2.89 (0.43), residues: 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 180 time to evaluate : 0.946 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 183 average time/residue: 0.1547 time to fit residues: 40.4425 Evaluate side-chains 172 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0626 time to fit residues: 1.1253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 6790 Z= 0.213 Angle : 0.984 13.464 9244 Z= 0.436 Chirality : 0.048 0.318 1136 Planarity : 0.004 0.042 1122 Dihedral : 4.500 22.466 924 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 1.12 % 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: 0.72 (0.29), residues: 876 helix: 1.37 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -2.90 (0.43), residues: 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 181 average time/residue: 0.1425 time to fit residues: 37.1022 Evaluate side-chains 171 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0739 time to fit residues: 1.3465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 7 optimal weight: 0.0060 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 6790 Z= 0.243 Angle : 1.038 17.227 9244 Z= 0.464 Chirality : 0.050 0.265 1136 Planarity : 0.004 0.042 1122 Dihedral : 4.517 22.047 924 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer Outliers : 0.28 % 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: 0.71 (0.29), residues: 876 helix: 1.36 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -2.88 (0.43), residues: 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 176 average time/residue: 0.1341 time to fit residues: 33.8914 Evaluate side-chains 172 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0648 time to fit residues: 1.2341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.084725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.075710 restraints weight = 36179.876| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 5.65 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 6790 Z= 0.251 Angle : 1.069 18.995 9244 Z= 0.475 Chirality : 0.049 0.270 1136 Planarity : 0.004 0.042 1122 Dihedral : 4.552 22.338 924 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 0.70 % 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: 0.59 (0.29), residues: 876 helix: 1.28 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.93 (0.43), residues: 192 =============================================================================== Job complete usr+sys time: 1541.94 seconds wall clock time: 28 minutes 47.11 seconds (1727.11 seconds total)