Starting phenix.real_space_refine on Thu Jul 18 19:51:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3d_41858/07_2024/8u3d_41858.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3d_41858/07_2024/8u3d_41858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3d_41858/07_2024/8u3d_41858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3d_41858/07_2024/8u3d_41858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3d_41858/07_2024/8u3d_41858.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3d_41858/07_2024/8u3d_41858.cif" } resolution = 2.83 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= 0.003 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2230 2.51 5 N 522 2.21 5 O 571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 481": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3338 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3338 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 1 Time building chain proxies: 3.25, per 1000 atoms: 0.97 Number of scatterers: 3338 At special positions: 0 Unit cell: (57.27, 71.38, 81.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 571 8.00 N 522 7.00 C 2230 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: 1.28 Conformation dependent library (CDL) restraints added in 657.6 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 37 through 68 removed outlier: 4.982A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 120 removed outlier: 4.874A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.893A pdb=" N GLY A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.911A pdb=" N LEU A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.884A pdb=" N ASP A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.502A pdb=" N LEU A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.678A pdb=" N ALA A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 224 removed outlier: 4.223A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 248 removed outlier: 4.134A pdb=" N PHE A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 288 through 319 removed outlier: 4.115A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 323 through 356 removed outlier: 3.836A pdb=" N LEU A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.661A pdb=" N GLY A 346 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 385 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 388 through 403 removed outlier: 3.889A pdb=" N THR A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 409 through 412 removed outlier: 3.539A pdb=" N ILE A 412 " --> pdb=" O GLY A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 412' Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.581A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 434 through 448 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.629A pdb=" N TRP A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 239 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.44 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: 684 1.45 - 1.57: 1759 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3440 Sorted by residual: bond pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.32e-02 5.74e+03 7.33e+00 bond pdb=" N LEU A 45 " pdb=" CA LEU A 45 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.37e+00 bond pdb=" CB THR A 400 " pdb=" CG2 THR A 400 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.13e+00 bond pdb=" N ALA A 43 " pdb=" CA ALA A 43 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.33e-02 5.65e+03 3.55e+00 bond pdb=" CA ALA A 43 " pdb=" CB ALA A 43 " ideal model delta sigma weight residual 1.530 1.499 0.031 1.68e-02 3.54e+03 3.42e+00 ... (remaining 3435 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.46: 93 106.46 - 113.38: 1873 113.38 - 120.29: 1384 120.29 - 127.20: 1291 127.20 - 134.11: 53 Bond angle restraints: 4694 Sorted by residual: angle pdb=" C THR A 434 " pdb=" N ILE A 435 " pdb=" CA ILE A 435 " ideal model delta sigma weight residual 120.24 122.92 -2.68 6.30e-01 2.52e+00 1.81e+01 angle pdb=" C ILE A 435 " pdb=" CA ILE A 435 " pdb=" CB ILE A 435 " ideal model delta sigma weight residual 114.35 110.35 4.00 1.06e+00 8.90e-01 1.42e+01 angle pdb=" N LEU A 45 " pdb=" CA LEU A 45 " pdb=" C LEU A 45 " ideal model delta sigma weight residual 112.90 108.56 4.34 1.31e+00 5.83e-01 1.10e+01 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" CB VAL A 177 " ideal model delta sigma weight residual 111.23 105.88 5.35 1.65e+00 3.67e-01 1.05e+01 angle pdb=" C PRO A 449 " pdb=" N ASP A 450 " pdb=" CA ASP A 450 " ideal model delta sigma weight residual 121.54 116.13 5.41 1.91e+00 2.74e-01 8.01e+00 ... (remaining 4689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 1772 17.10 - 34.19: 140 34.19 - 51.29: 20 51.29 - 68.38: 2 68.38 - 85.48: 3 Dihedral angle restraints: 1937 sinusoidal: 716 harmonic: 1221 Sorted by residual: dihedral pdb=" CA PHE A 358 " pdb=" C PHE A 358 " pdb=" N SER A 359 " pdb=" CA SER A 359 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASP A 450 " pdb=" C ASP A 450 " pdb=" N ASN A 451 " pdb=" CA ASN A 451 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA TRP A 246 " pdb=" C TRP A 246 " pdb=" N LEU A 247 " pdb=" CA LEU A 247 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 1934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 335 0.044 - 0.089: 154 0.089 - 0.133: 38 0.133 - 0.177: 5 0.177 - 0.221: 1 Chirality restraints: 533 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LEU A 289 " pdb=" N LEU A 289 " pdb=" C LEU A 289 " pdb=" CB LEU A 289 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 530 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO A 290 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " 0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 375 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 163 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.025 5.00e-02 4.00e+02 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 988 2.81 - 3.33: 3269 3.33 - 3.85: 5720 3.85 - 4.38: 7053 4.38 - 4.90: 11807 Nonbonded interactions: 28837 Sorted by model distance: nonbonded pdb=" OG1 THR A 304 " pdb=" OD1 ASN A 467 " model vdw 2.284 2.440 nonbonded pdb=" O SER A 213 " pdb=" OG SER A 217 " model vdw 2.301 2.440 nonbonded pdb=" O THR A 452 " pdb=" N GLU A 455 " model vdw 2.315 2.520 nonbonded pdb=" OH TYR A 40 " pdb=" OE2 GLU A 194 " model vdw 2.329 2.440 nonbonded pdb=" NZ LYS A 317 " pdb=" OE2 GLU A 318 " model vdw 2.345 2.520 ... (remaining 28832 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: 1.260 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.840 Find NCS groups from input model: 0.040 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.009 0.075 3440 Z= 0.555 Angle : 0.781 7.654 4694 Z= 0.461 Chirality : 0.052 0.221 533 Planarity : 0.006 0.055 569 Dihedral : 12.533 85.479 1161 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.35), residues: 423 helix: -1.21 (0.25), residues: 326 sheet: None (None), residues: 0 loop : -2.21 (0.55), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 244 HIS 0.011 0.003 HIS A 298 PHE 0.016 0.002 PHE A 299 TYR 0.021 0.002 TYR A 335 ARG 0.006 0.001 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.357 Fit side-chains REVERT: A 239 PHE cc_start: 0.7041 (t80) cc_final: 0.6678 (m-10) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.8876 time to fit residues: 33.5088 Evaluate side-chains 32 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 351 ASN A 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3440 Z= 0.169 Angle : 0.560 8.606 4694 Z= 0.294 Chirality : 0.042 0.124 533 Planarity : 0.006 0.046 569 Dihedral : 4.800 19.868 455 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.27 % Allowed : 8.81 % Favored : 88.92 % 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: -0.33 (0.40), residues: 423 helix: 0.29 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.78 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 244 HIS 0.005 0.001 HIS A 298 PHE 0.015 0.001 PHE A 232 TYR 0.014 0.001 TYR A 335 ARG 0.001 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.342 Fit side-chains REVERT: A 239 PHE cc_start: 0.7035 (t80) cc_final: 0.6650 (m-10) outliers start: 8 outliers final: 1 residues processed: 40 average time/residue: 0.7653 time to fit residues: 32.3029 Evaluate side-chains 29 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS A 413 ASN A 467 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3440 Z= 0.217 Angle : 0.567 8.386 4694 Z= 0.295 Chirality : 0.043 0.131 533 Planarity : 0.006 0.050 569 Dihedral : 4.647 17.262 455 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.27 % Allowed : 10.80 % Favored : 86.93 % 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: 0.34 (0.40), residues: 423 helix: 0.80 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.70 (0.55), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 PHE 0.013 0.002 PHE A 299 TYR 0.009 0.001 TYR A 335 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.368 Fit side-chains REVERT: A 239 PHE cc_start: 0.7037 (t80) cc_final: 0.6650 (m-10) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.7803 time to fit residues: 29.6267 Evaluate side-chains 33 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 342 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 38 optimal weight: 0.0970 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 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 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3440 Z= 0.169 Angle : 0.535 8.036 4694 Z= 0.277 Chirality : 0.041 0.119 533 Planarity : 0.006 0.053 569 Dihedral : 4.465 16.533 455 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.27 % Allowed : 11.65 % Favored : 86.08 % 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 (0.41), residues: 423 helix: 1.17 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.50 (0.56), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.015 0.001 PHE A 384 TYR 0.007 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.274 Fit side-chains REVERT: A 207 GLN cc_start: 0.8384 (mp10) cc_final: 0.8084 (mm-40) REVERT: A 239 PHE cc_start: 0.7058 (t80) cc_final: 0.6652 (m-10) REVERT: A 417 ILE cc_start: 0.7856 (tp) cc_final: 0.7597 (tt) outliers start: 8 outliers final: 3 residues processed: 38 average time/residue: 0.6083 time to fit residues: 24.3844 Evaluate side-chains 34 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 400 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 0.0570 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3440 Z= 0.179 Angle : 0.542 7.951 4694 Z= 0.279 Chirality : 0.042 0.119 533 Planarity : 0.006 0.054 569 Dihedral : 4.404 15.024 455 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.27 % Allowed : 12.78 % Favored : 84.94 % 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: 1.08 (0.41), residues: 423 helix: 1.31 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.42 (0.57), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.017 0.001 PHE A 384 TYR 0.008 0.001 TYR A 335 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.360 Fit side-chains REVERT: A 207 GLN cc_start: 0.8418 (mp10) cc_final: 0.8104 (mm-40) REVERT: A 239 PHE cc_start: 0.7069 (t80) cc_final: 0.6654 (m-10) REVERT: A 250 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6697 (m-30) REVERT: A 417 ILE cc_start: 0.7852 (tp) cc_final: 0.7501 (tp) outliers start: 8 outliers final: 6 residues processed: 34 average time/residue: 0.7849 time to fit residues: 28.1624 Evaluate side-chains 37 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 400 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.0010 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3440 Z= 0.167 Angle : 0.532 7.922 4694 Z= 0.273 Chirality : 0.041 0.116 533 Planarity : 0.005 0.055 569 Dihedral : 4.317 14.908 455 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.12 % Allowed : 13.35 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.41), residues: 423 helix: 1.57 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.15 (0.56), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 PHE 0.020 0.001 PHE A 384 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.365 Fit side-chains REVERT: A 207 GLN cc_start: 0.8419 (mp10) cc_final: 0.8105 (mm-40) REVERT: A 239 PHE cc_start: 0.7056 (t80) cc_final: 0.6652 (m-10) REVERT: A 250 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6689 (m-30) REVERT: A 417 ILE cc_start: 0.7881 (tp) cc_final: 0.7541 (tp) outliers start: 11 outliers final: 6 residues processed: 39 average time/residue: 0.6765 time to fit residues: 27.8877 Evaluate side-chains 37 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 400 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 0.037 3440 Z= 0.197 Angle : 0.551 7.856 4694 Z= 0.283 Chirality : 0.042 0.131 533 Planarity : 0.006 0.055 569 Dihedral : 4.344 15.132 455 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.56 % Allowed : 15.06 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.41), residues: 423 helix: 1.53 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.04 (0.56), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 PHE 0.023 0.002 PHE A 384 TYR 0.009 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 0.387 Fit side-chains REVERT: A 207 GLN cc_start: 0.8424 (mp10) cc_final: 0.8104 (mm-40) REVERT: A 239 PHE cc_start: 0.7062 (t80) cc_final: 0.6660 (m-10) REVERT: A 417 ILE cc_start: 0.7893 (tp) cc_final: 0.7553 (tp) outliers start: 9 outliers final: 5 residues processed: 34 average time/residue: 0.8618 time to fit residues: 30.8374 Evaluate side-chains 34 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 400 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3440 Z= 0.216 Angle : 0.558 7.801 4694 Z= 0.287 Chirality : 0.043 0.127 533 Planarity : 0.006 0.055 569 Dihedral : 4.400 15.235 455 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.84 % Allowed : 14.49 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.41), residues: 423 helix: 1.50 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.04 (0.57), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.025 0.002 PHE A 384 TYR 0.009 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.384 Fit side-chains REVERT: A 239 PHE cc_start: 0.7078 (t80) cc_final: 0.6679 (m-10) REVERT: A 417 ILE cc_start: 0.7866 (tp) cc_final: 0.7519 (tp) outliers start: 10 outliers final: 5 residues processed: 35 average time/residue: 0.7152 time to fit residues: 26.4563 Evaluate side-chains 34 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 400 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3440 Z= 0.170 Angle : 0.537 7.902 4694 Z= 0.275 Chirality : 0.041 0.119 533 Planarity : 0.006 0.055 569 Dihedral : 4.297 14.902 455 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.70 % Allowed : 16.19 % Favored : 82.10 % 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: 1.52 (0.41), residues: 423 helix: 1.60 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.03 (0.57), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 PHE 0.026 0.001 PHE A 384 TYR 0.007 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.364 Fit side-chains REVERT: A 239 PHE cc_start: 0.7065 (t80) cc_final: 0.6667 (m-10) REVERT: A 417 ILE cc_start: 0.7857 (tp) cc_final: 0.7514 (tp) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 0.8142 time to fit residues: 31.6377 Evaluate side-chains 37 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3440 Z= 0.157 Angle : 0.532 7.915 4694 Z= 0.272 Chirality : 0.041 0.118 533 Planarity : 0.005 0.056 569 Dihedral : 4.221 14.763 455 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.99 % Allowed : 16.19 % Favored : 81.82 % 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: 1.55 (0.41), residues: 423 helix: 1.68 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.27 (0.57), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.002 0.000 HIS A 298 PHE 0.028 0.001 PHE A 384 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.669 Fit side-chains REVERT: A 239 PHE cc_start: 0.7060 (t80) cc_final: 0.6664 (m-10) REVERT: A 417 ILE cc_start: 0.7746 (tp) cc_final: 0.7474 (tp) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.8942 time to fit residues: 36.8389 Evaluate side-chains 39 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.097994 restraints weight = 3902.068| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.83 r_work: 0.2758 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3440 Z= 0.182 Angle : 0.541 7.836 4694 Z= 0.278 Chirality : 0.042 0.115 533 Planarity : 0.005 0.055 569 Dihedral : 4.253 14.920 455 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.99 % Allowed : 16.19 % Favored : 81.82 % 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: 1.61 (0.41), residues: 423 helix: 1.71 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.14 (0.57), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 PHE 0.027 0.001 PHE A 384 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.70 seconds wall clock time: 25 minutes 57.39 seconds (1557.39 seconds total)