Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 18:23:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2023/7xq0_33387_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2023/7xq0_33387.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2023/7xq0_33387_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2023/7xq0_33387_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2023/7xq0_33387_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2023/7xq0_33387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2023/7xq0_33387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2023/7xq0_33387_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/07_2023/7xq0_33387_neut_updated.pdb" } resolution = 3.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 10 5.16 5 C 2189 2.51 5 N 553 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 3320 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3320 Classifications: {'RNA': 2, 'peptide': 402} Link IDs: {'PTRANS': 14, 'TRANS': 387, 'rna3p': 1, None: 1} Not linked: pdbres="ARG A 456 " pdbres="2BA A 601 " Chain breaks: 2 Time building chain proxies: 2.08, per 1000 atoms: 0.63 Number of scatterers: 3320 At special positions: 0 Unit cell: (78, 75, 67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 4 15.00 O 564 8.00 N 553 7.00 C 2189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 487.3 milliseconds 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 0 sheets defined 75.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 20 through 26 removed outlier: 3.621A pdb=" N TRP A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 40 removed outlier: 4.415A pdb=" N GLN A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 61 through 64 No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 69 through 89 removed outlier: 3.539A pdb=" N TYR A 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 79 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 80 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL A 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.746A pdb=" N LEU A 86 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 87 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR A 89 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 112 removed outlier: 3.562A pdb=" N SER A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 143 removed outlier: 4.926A pdb=" N ILE A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.686A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 removed outlier: 3.712A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 4.104A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.540A pdb=" N LEU A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 295 removed outlier: 4.142A pdb=" N LEU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 293 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.797A pdb=" N THR A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 336 through 355 Processing helix chain 'A' and resid 359 through 376 removed outlier: 3.648A pdb=" N ILE A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TRP A 363 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 366 " --> pdb=" O TRP A 363 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 368 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 370 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU A 371 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 374 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 393 through 417 removed outlier: 3.765A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 455 removed outlier: 3.962A pdb=" N ILE A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 516 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: 0.82 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 973 1.34 - 1.45: 637 1.45 - 1.57: 1781 1.57 - 1.69: 12 1.69 - 1.80: 18 Bond restraints: 3421 Sorted by residual: bond pdb="C1'1 2BA A 601 " pdb="C2'1 2BA A 601 " ideal model delta sigma weight residual 1.674 1.294 0.380 2.00e-02 2.50e+03 3.61e+02 bond pdb="C1'1 2BA A 602 " pdb="C2'1 2BA A 602 " ideal model delta sigma weight residual 1.674 1.297 0.377 2.00e-02 2.50e+03 3.56e+02 bond pdb="C1'1 2BA A 601 " pdb="O4'1 2BA A 601 " ideal model delta sigma weight residual 1.306 1.617 -0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb="C1'1 2BA A 602 " pdb="O4'1 2BA A 602 " ideal model delta sigma weight residual 1.306 1.616 -0.310 2.00e-02 2.50e+03 2.41e+02 bond pdb="C2'1 2BA A 602 " pdb="C3'1 2BA A 602 " ideal model delta sigma weight residual 1.239 1.541 -0.302 2.00e-02 2.50e+03 2.28e+02 ... (remaining 3416 not shown) Histogram of bond angle deviations from ideal: 100.02 - 107.16: 115 107.16 - 114.29: 1981 114.29 - 121.43: 1904 121.43 - 128.57: 642 128.57 - 135.70: 39 Bond angle restraints: 4681 Sorted by residual: angle pdb=" C81 2BA A 601 " pdb=" N91 2BA A 601 " pdb="C1'1 2BA A 601 " ideal model delta sigma weight residual 85.30 119.75 -34.45 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C81 2BA A 602 " pdb=" N91 2BA A 602 " pdb="C1'1 2BA A 602 " ideal model delta sigma weight residual 85.30 119.60 -34.30 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C1' 2BA A 602 " pdb=" N9 2BA A 602 " pdb=" C8 2BA A 602 " ideal model delta sigma weight residual 92.12 118.28 -26.16 3.00e+00 1.11e-01 7.61e+01 angle pdb=" C1' 2BA A 601 " pdb=" N9 2BA A 601 " pdb=" C8 2BA A 601 " ideal model delta sigma weight residual 92.12 117.50 -25.38 3.00e+00 1.11e-01 7.16e+01 angle pdb=" C41 2BA A 601 " pdb=" N91 2BA A 601 " pdb="C1'1 2BA A 601 " ideal model delta sigma weight residual 109.25 132.25 -23.00 3.00e+00 1.11e-01 5.88e+01 ... (remaining 4676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 1782 17.91 - 35.82: 110 35.82 - 53.73: 21 53.73 - 71.64: 4 71.64 - 89.55: 4 Dihedral angle restraints: 1921 sinusoidal: 738 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA VAL A 418 " pdb=" C VAL A 418 " pdb=" N SER A 419 " pdb=" CA SER A 419 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" C5' 2BA A 601 " pdb=" O5' 2BA A 601 " pdb=" P 2BA A 601 " pdb="O3'1 2BA A 601 " ideal model delta sinusoidal sigma weight residual 147.86 58.31 89.55 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 1918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 340 0.040 - 0.080: 158 0.080 - 0.120: 34 0.120 - 0.160: 7 0.160 - 0.200: 3 Chirality restraints: 542 Sorted by residual: chirality pdb=" CA LEU A 210 " pdb=" N LEU A 210 " pdb=" C LEU A 210 " pdb=" CB LEU A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA THR A 93 " pdb=" N THR A 93 " pdb=" C THR A 93 " pdb=" CB THR A 93 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb="C3'1 2BA A 601 " pdb="C2'1 2BA A 601 " pdb="C4'1 2BA A 601 " pdb="O3'1 2BA A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 539 not shown) Planarity restraints: 552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 71 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C VAL A 71 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL A 71 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 72 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO A 82 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.037 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO A 70 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.031 5.00e-02 4.00e+02 ... (remaining 549 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 747 2.77 - 3.30: 3036 3.30 - 3.83: 5812 3.83 - 4.37: 7360 4.37 - 4.90: 11924 Nonbonded interactions: 28879 Sorted by model distance: nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.232 2.440 nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.258 2.440 nonbonded pdb=" O1P 2BA A 601 " pdb=" N6 2BA A 602 " model vdw 2.328 2.520 nonbonded pdb=" O ARG A 61 " pdb=" OG1 THR A 65 " model vdw 2.336 2.440 nonbonded pdb=" OG SER A 392 " pdb=" OE1 GLU A 394 " model vdw 2.339 2.440 ... (remaining 28874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.620 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: 7.120 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.910 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.018 0.380 3421 Z= 1.178 Angle : 1.346 34.450 4681 Z= 0.590 Chirality : 0.047 0.200 542 Planarity : 0.006 0.057 552 Dihedral : 13.276 89.547 1161 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 0.86 % 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: -6.72 (0.21), residues: 398 helix: -4.46 (0.12), residues: 313 sheet: None (None), residues: 0 loop : -3.02 (0.49), residues: 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.333 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 56 average time/residue: 0.9102 time to fit residues: 53.0659 Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.0170 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 277 ASN A 293 ASN A 431 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3421 Z= 0.191 Angle : 0.962 24.995 4681 Z= 0.389 Chirality : 0.038 0.106 542 Planarity : 0.005 0.034 552 Dihedral : 7.391 69.250 458 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 2.88 % 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: -3.53 (0.33), residues: 398 helix: -2.13 (0.23), residues: 318 sheet: None (None), residues: 0 loop : -2.22 (0.59), residues: 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.373 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 50 average time/residue: 0.6630 time to fit residues: 35.1473 Evaluate side-chains 39 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.0050 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 3421 Z= 0.152 Angle : 0.939 24.784 4681 Z= 0.364 Chirality : 0.036 0.116 542 Planarity : 0.003 0.025 552 Dihedral : 6.545 52.332 458 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 2.31 % 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: -1.26 (0.40), residues: 398 helix: -0.42 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -1.95 (0.61), residues: 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.359 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 0.6103 time to fit residues: 34.3861 Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.0010 chunk 36 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 3421 Z= 0.140 Angle : 0.924 24.761 4681 Z= 0.356 Chirality : 0.037 0.173 542 Planarity : 0.003 0.022 552 Dihedral : 6.164 50.888 458 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 2.88 % 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: -0.26 (0.42), residues: 398 helix: 0.32 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -1.75 (0.61), residues: 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.359 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 49 average time/residue: 0.6523 time to fit residues: 33.8820 Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0346 time to fit residues: 0.5555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3421 Z= 0.202 Angle : 0.935 24.783 4681 Z= 0.361 Chirality : 0.039 0.142 542 Planarity : 0.003 0.021 552 Dihedral : 6.049 48.982 458 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 2.31 % 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: 0.17 (0.43), residues: 398 helix: 0.62 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -1.59 (0.62), residues: 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.374 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 0.6101 time to fit residues: 29.9082 Evaluate side-chains 40 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.0370 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.0570 chunk 12 optimal weight: 0.0970 chunk 20 optimal weight: 0.0570 chunk 37 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.1092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 3421 Z= 0.121 Angle : 0.932 24.701 4681 Z= 0.354 Chirality : 0.037 0.189 542 Planarity : 0.003 0.024 552 Dihedral : 5.822 50.361 458 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.43), residues: 398 helix: 0.99 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -1.49 (0.62), residues: 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.357 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.6134 time to fit residues: 30.0550 Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.4909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3421 Z= 0.203 Angle : 0.949 24.854 4681 Z= 0.365 Chirality : 0.040 0.165 542 Planarity : 0.003 0.022 552 Dihedral : 6.015 48.078 458 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 2.02 % 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 (0.42), residues: 398 helix: 1.02 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -1.57 (0.61), residues: 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.356 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 0.6395 time to fit residues: 29.2880 Evaluate side-chains 39 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.3980 chunk 30 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3421 Z= 0.195 Angle : 0.947 24.773 4681 Z= 0.365 Chirality : 0.040 0.200 542 Planarity : 0.003 0.023 552 Dihedral : 5.996 47.730 458 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 1.73 % 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 (0.42), residues: 398 helix: 1.13 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -1.51 (0.59), residues: 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.368 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.5750 time to fit residues: 25.9435 Evaluate side-chains 39 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 3421 Z= 0.250 Angle : 0.963 24.756 4681 Z= 0.374 Chirality : 0.041 0.194 542 Planarity : 0.003 0.026 552 Dihedral : 6.062 46.763 458 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 0.86 % 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 (0.42), residues: 398 helix: 1.07 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -1.50 (0.59), residues: 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.365 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.7579 time to fit residues: 32.8342 Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.0170 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3421 Z= 0.199 Angle : 0.949 24.764 4681 Z= 0.367 Chirality : 0.040 0.214 542 Planarity : 0.003 0.026 552 Dihedral : 6.002 46.728 458 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 1.44 % 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: 0.88 (0.42), residues: 398 helix: 1.15 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -1.50 (0.59), residues: 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.412 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.7692 time to fit residues: 34.1446 Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.093316 restraints weight = 3887.664| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.82 r_work: 0.2880 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3421 Z= 0.226 Angle : 0.956 24.683 4681 Z= 0.370 Chirality : 0.041 0.210 542 Planarity : 0.003 0.027 552 Dihedral : 6.033 46.659 458 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 1.73 % 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 (0.42), residues: 398 helix: 1.14 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -1.51 (0.59), residues: 82 =============================================================================== Job complete usr+sys time: 1443.38 seconds wall clock time: 26 minutes 54.70 seconds (1614.70 seconds total)