Starting phenix.real_space_refine on Sun Mar 10 16:37:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/03_2024/7xq0_33387_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/03_2024/7xq0_33387.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/03_2024/7xq0_33387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/03_2024/7xq0_33387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/03_2024/7xq0_33387_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq0_33387/03_2024/7xq0_33387_neut_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-dev-5265/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: 2.36, per 1000 atoms: 0.71 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: 1.25 Conformation dependent library (CDL) restraints added in 591.6 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: 0.67 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: 0.86 Time building geometry restraints manager: 1.37 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 1.532 1.294 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb="C1'1 2BA A 602 " pdb="C2'1 2BA A 602 " ideal model delta sigma weight residual 1.532 1.297 0.235 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' 2BA A 601 " pdb=" C2' 2BA A 601 " ideal model delta sigma weight residual 1.541 1.317 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C1' 2BA A 602 " pdb=" C2' 2BA A 602 " ideal model delta sigma weight residual 1.541 1.318 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb="C1'1 2BA A 601 " pdb="O4'1 2BA A 601 " ideal model delta sigma weight residual 1.408 1.617 -0.209 2.00e-02 2.50e+03 1.09e+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=" CA VAL A 380 " pdb=" C VAL A 380 " pdb=" N PRO A 381 " ideal model delta sigma weight residual 120.83 116.29 4.54 6.10e-01 2.69e+00 5.53e+01 angle pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 112.23 105.18 7.05 1.26e+00 6.30e-01 3.13e+01 angle pdb=" O1P 2BA A 601 " pdb=" P 2BA A 601 " pdb=" O2P 2BA A 601 " ideal model delta sigma weight residual 121.18 104.63 16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O1P 2BA A 602 " pdb=" P 2BA A 602 " pdb=" O2P 2BA A 602 " ideal model delta sigma weight residual 121.18 104.64 16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb="O1P1 2BA A 602 " pdb=" P1 2BA A 602 " pdb="O2P1 2BA A 602 " ideal model delta sigma weight residual 122.22 106.86 15.36 3.00e+00 1.11e-01 2.62e+01 ... (remaining 4676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 1870 17.70 - 35.39: 137 35.39 - 53.09: 24 53.09 - 70.79: 3 70.79 - 88.48: 3 Dihedral angle restraints: 2037 sinusoidal: 854 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=" CA TRP A 363 " pdb=" C TRP A 363 " pdb=" N LEU A 364 " pdb=" CA LEU A 364 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2034 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.099: 514 0.099 - 0.198: 23 0.198 - 0.297: 3 0.297 - 0.396: 0 0.396 - 0.494: 2 Chirality restraints: 542 Sorted by residual: chirality pdb=" C2' 2BA A 602 " pdb=" C1' 2BA A 602 " pdb=" C3' 2BA A 602 " pdb=" O2' 2BA A 602 " both_signs ideal model delta sigma weight residual False -2.80 -2.31 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" C2' 2BA A 601 " pdb=" C1' 2BA A 601 " pdb=" C3' 2BA A 601 " pdb=" O2' 2BA A 601 " both_signs ideal model delta sigma weight residual False -2.80 -2.34 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb="C2'1 2BA A 602 " pdb="C1'1 2BA A 602 " pdb="C3'1 2BA A 602 " pdb="O2'1 2BA A 602 " both_signs ideal model delta sigma weight residual False -2.67 -2.39 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.730 Find NCS groups from input model: 0.080 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:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.440 ------------------------------------------------------------------------------- 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 : 0.014 0.238 3421 Z= 0.947 Angle : 1.263 16.547 4681 Z= 0.569 Chirality : 0.057 0.494 542 Planarity : 0.006 0.057 552 Dihedral : 13.005 88.484 1277 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 % Allowed : 8.36 % Favored : 90.78 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.011 0.001 PHE A 37 TYR 0.009 0.002 TYR A 76 ARG 0.005 0.000 ARG A 42 *********************** 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 : 0.364 Fit side-chains REVERT: A 26 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7168 (mmp-170) REVERT: A 62 GLU cc_start: 0.7399 (pp20) cc_final: 0.6862 (tm-30) REVERT: A 122 MET cc_start: 0.8531 (tmm) cc_final: 0.8278 (ttp) REVERT: A 333 ARG cc_start: 0.7603 (tmt170) cc_final: 0.7023 (tpt-90) REVERT: A 416 PHE cc_start: 0.8211 (t80) cc_final: 0.7976 (t80) REVERT: A 451 MET cc_start: 0.6313 (mmt) cc_final: 0.6057 (mmt) outliers start: 3 outliers final: 0 residues processed: 56 average time/residue: 0.8868 time to fit residues: 51.7401 Evaluate side-chains 39 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 36 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 266 GLN A 293 ASN A 431 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3421 Z= 0.187 Angle : 0.551 6.330 4681 Z= 0.281 Chirality : 0.037 0.111 542 Planarity : 0.005 0.033 552 Dihedral : 6.142 24.651 574 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.17 % Allowed : 11.82 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.33), residues: 398 helix: -2.08 (0.23), residues: 318 sheet: None (None), residues: 0 loop : -2.17 (0.58), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.009 0.001 PHE A 212 TYR 0.009 0.001 TYR A 35 ARG 0.002 0.000 ARG A 133 *********************** 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 57 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.351 Fit side-chains REVERT: A 26 ARG cc_start: 0.7354 (mtp85) cc_final: 0.6986 (mmp-170) REVERT: A 62 GLU cc_start: 0.7405 (pp20) cc_final: 0.6834 (pm20) REVERT: A 148 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6702 (mpp80) REVERT: A 333 ARG cc_start: 0.7597 (tmt170) cc_final: 0.7024 (tpt-90) REVERT: A 416 PHE cc_start: 0.8203 (t80) cc_final: 0.7969 (t80) outliers start: 11 outliers final: 2 residues processed: 54 average time/residue: 0.6340 time to fit residues: 36.2632 Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.0050 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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: 0.7577 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3421 Z= 0.183 Angle : 0.531 7.467 4681 Z= 0.261 Chirality : 0.037 0.116 542 Planarity : 0.003 0.025 552 Dihedral : 5.744 25.713 574 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.59 % Allowed : 14.70 % Favored : 82.71 % 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: -1.42 (0.40), residues: 398 helix: -0.53 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -2.06 (0.60), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.012 0.001 PHE A 447 TYR 0.009 0.001 TYR A 438 ARG 0.001 0.000 ARG A 429 *********************** 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 54 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.352 Fit side-chains REVERT: A 26 ARG cc_start: 0.7332 (mtp85) cc_final: 0.6959 (mmp-170) REVERT: A 62 GLU cc_start: 0.7403 (pp20) cc_final: 0.6847 (pm20) REVERT: A 148 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6710 (mpp80) REVERT: A 333 ARG cc_start: 0.7600 (tmt170) cc_final: 0.7027 (tpt-90) REVERT: A 416 PHE cc_start: 0.8195 (t80) cc_final: 0.7975 (t80) outliers start: 9 outliers final: 2 residues processed: 51 average time/residue: 0.6797 time to fit residues: 36.5940 Evaluate side-chains 44 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 258 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.0570 chunk 36 optimal weight: 0.0010 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 0.4104 ------------------------------------------------------------------------------- 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: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3421 Z= 0.158 Angle : 0.498 7.251 4681 Z= 0.244 Chirality : 0.037 0.161 542 Planarity : 0.003 0.020 552 Dihedral : 5.545 23.963 574 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.59 % Allowed : 15.56 % Favored : 81.84 % 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: -0.37 (0.42), residues: 398 helix: 0.23 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -1.73 (0.60), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.007 0.001 PHE A 372 TYR 0.009 0.001 TYR A 35 ARG 0.001 0.000 ARG A 264 *********************** 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 55 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.329 Fit side-chains REVERT: A 26 ARG cc_start: 0.7342 (mtp85) cc_final: 0.6950 (mmp-170) REVERT: A 62 GLU cc_start: 0.7409 (pp20) cc_final: 0.6844 (pm20) REVERT: A 148 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6692 (mpp80) REVERT: A 187 TYR cc_start: 0.8487 (m-80) cc_final: 0.8139 (m-80) REVERT: A 333 ARG cc_start: 0.7539 (tmt170) cc_final: 0.6986 (tpt-90) REVERT: A 451 MET cc_start: 0.6587 (mmt) cc_final: 0.6345 (mpp) outliers start: 9 outliers final: 2 residues processed: 53 average time/residue: 0.6645 time to fit residues: 37.2081 Evaluate side-chains 46 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 277 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.0000 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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: 0.7570 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3421 Z= 0.182 Angle : 0.518 8.945 4681 Z= 0.250 Chirality : 0.038 0.141 542 Planarity : 0.003 0.020 552 Dihedral : 5.559 24.380 574 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.88 % Allowed : 17.00 % Favored : 80.12 % 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: 0.12 (0.42), residues: 398 helix: 0.59 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -1.62 (0.60), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.011 0.001 PHE A 84 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 429 *********************** 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 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.320 Fit side-chains REVERT: A 26 ARG cc_start: 0.7345 (mtp85) cc_final: 0.6947 (mmp-170) REVERT: A 62 GLU cc_start: 0.7422 (pp20) cc_final: 0.6869 (pm20) REVERT: A 148 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6756 (mpp80) REVERT: A 187 TYR cc_start: 0.8449 (m-80) cc_final: 0.8079 (m-80) REVERT: A 333 ARG cc_start: 0.7544 (tmt170) cc_final: 0.6995 (tpt-90) REVERT: A 416 PHE cc_start: 0.7533 (t80) cc_final: 0.7248 (t80) REVERT: A 451 MET cc_start: 0.6489 (mmt) cc_final: 0.6281 (mpp) outliers start: 10 outliers final: 3 residues processed: 51 average time/residue: 0.7277 time to fit residues: 39.1918 Evaluate side-chains 45 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 271 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7582 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3421 Z= 0.211 Angle : 0.540 9.072 4681 Z= 0.258 Chirality : 0.039 0.187 542 Planarity : 0.003 0.021 552 Dihedral : 5.634 25.287 574 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.17 % Allowed : 17.29 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.42), residues: 398 helix: 0.70 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -1.75 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.007 0.001 PHE A 372 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 429 *********************** 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 51 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.331 Fit side-chains REVERT: A 26 ARG cc_start: 0.7349 (mtp85) cc_final: 0.6944 (mmp-170) REVERT: A 62 GLU cc_start: 0.7411 (pp20) cc_final: 0.6873 (pm20) REVERT: A 148 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6767 (mpp80) REVERT: A 333 ARG cc_start: 0.7590 (tmt170) cc_final: 0.6964 (tpt-90) REVERT: A 416 PHE cc_start: 0.7474 (t80) cc_final: 0.7222 (t80) outliers start: 11 outliers final: 4 residues processed: 49 average time/residue: 0.7002 time to fit residues: 36.1752 Evaluate side-chains 44 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 271 SER 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: 0.9980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.0060 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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: 0.7561 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3421 Z= 0.160 Angle : 0.518 8.817 4681 Z= 0.250 Chirality : 0.038 0.176 542 Planarity : 0.003 0.021 552 Dihedral : 5.491 25.282 574 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.88 % Allowed : 17.58 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.42), residues: 398 helix: 0.90 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -1.73 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.019 0.001 PHE A 447 TYR 0.009 0.001 TYR A 35 ARG 0.001 0.000 ARG A 264 *********************** 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 52 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.359 Fit side-chains REVERT: A 26 ARG cc_start: 0.7347 (mtp85) cc_final: 0.6935 (mmp-170) REVERT: A 62 GLU cc_start: 0.7410 (pp20) cc_final: 0.6855 (pm20) REVERT: A 148 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6778 (mpp80) REVERT: A 187 TYR cc_start: 0.8448 (m-80) cc_final: 0.8074 (m-80) REVERT: A 333 ARG cc_start: 0.7531 (tmt170) cc_final: 0.6942 (tpt-90) REVERT: A 416 PHE cc_start: 0.7394 (t80) cc_final: 0.7156 (t80) outliers start: 10 outliers final: 4 residues processed: 49 average time/residue: 0.7477 time to fit residues: 38.5582 Evaluate side-chains 45 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 271 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.0070 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 11 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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: 0.7548 moved from start: 0.2649 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= 0.147 Angle : 0.506 9.397 4681 Z= 0.243 Chirality : 0.038 0.205 542 Planarity : 0.003 0.022 552 Dihedral : 5.398 25.492 574 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.02 % Allowed : 18.16 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.42), residues: 398 helix: 1.06 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -1.57 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.000 0.000 HIS A 114 PHE 0.006 0.001 PHE A 372 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 264 *********************** 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 47 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.342 Fit side-chains REVERT: A 26 ARG cc_start: 0.7338 (mtp85) cc_final: 0.6920 (mmp-170) REVERT: A 62 GLU cc_start: 0.7419 (pp20) cc_final: 0.6828 (pm20) REVERT: A 148 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6780 (mpp80) REVERT: A 187 TYR cc_start: 0.8440 (m-80) cc_final: 0.8072 (m-80) REVERT: A 333 ARG cc_start: 0.7530 (tmt170) cc_final: 0.6940 (tpt-90) REVERT: A 416 PHE cc_start: 0.7342 (t80) cc_final: 0.7116 (t80) REVERT: A 451 MET cc_start: 0.6438 (mmt) cc_final: 0.6218 (mpp) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.8200 time to fit residues: 38.6742 Evaluate side-chains 46 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 271 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5942 ------------------------------------------------------------------------------- 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: 0.7573 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3421 Z= 0.200 Angle : 0.531 8.973 4681 Z= 0.254 Chirality : 0.040 0.190 542 Planarity : 0.003 0.024 552 Dihedral : 5.561 26.562 574 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.59 % Allowed : 17.87 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.42), residues: 398 helix: 1.07 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -1.57 (0.61), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.016 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.001 0.000 ARG A 256 *********************** 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 51 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.350 Fit side-chains REVERT: A 26 ARG cc_start: 0.7349 (mtp85) cc_final: 0.6945 (mmp-170) REVERT: A 62 GLU cc_start: 0.7405 (pp20) cc_final: 0.6823 (pm20) REVERT: A 148 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6775 (mpp80) REVERT: A 289 HIS cc_start: 0.8684 (m-70) cc_final: 0.8309 (m170) REVERT: A 333 ARG cc_start: 0.7521 (tmt170) cc_final: 0.6931 (tpt-90) REVERT: A 416 PHE cc_start: 0.7367 (t80) cc_final: 0.7131 (t80) outliers start: 9 outliers final: 3 residues processed: 49 average time/residue: 0.8605 time to fit residues: 44.3208 Evaluate side-chains 44 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 271 SER 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: 0.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.2681 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= 0.183 Angle : 0.536 9.117 4681 Z= 0.257 Chirality : 0.039 0.208 542 Planarity : 0.003 0.026 552 Dihedral : 5.529 26.589 574 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.02 % Allowed : 19.02 % Favored : 78.96 % 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: 0.87 (0.42), residues: 398 helix: 1.14 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -1.50 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.024 0.001 PHE A 447 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 429 ********************** 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 48 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.368 Fit side-chains REVERT: A 26 ARG cc_start: 0.7344 (mtp85) cc_final: 0.6938 (mmp-170) REVERT: A 62 GLU cc_start: 0.7419 (pp20) cc_final: 0.6811 (pm20) REVERT: A 148 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6769 (mpp80) REVERT: A 333 ARG cc_start: 0.7502 (tmt170) cc_final: 0.6912 (tpt-90) REVERT: A 416 PHE cc_start: 0.7332 (t80) cc_final: 0.7101 (t80) REVERT: A 451 MET cc_start: 0.7122 (mpp) cc_final: 0.6759 (mmt) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.8315 time to fit residues: 39.2485 Evaluate side-chains 44 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 271 SER 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: 0.6980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.112348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.094726 restraints weight = 3751.627| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.84 r_work: 0.2900 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2641 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= 0.211 Angle : 0.547 9.038 4681 Z= 0.263 Chirality : 0.040 0.206 542 Planarity : 0.003 0.026 552 Dihedral : 5.613 27.117 574 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.73 % Allowed : 19.02 % Favored : 79.25 % 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: 1.12 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.48 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.026 0.001 PHE A 447 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1479.15 seconds wall clock time: 27 minutes 23.63 seconds (1643.63 seconds total)