Starting phenix.real_space_refine on Sun Mar 10 15:53:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/03_2024/8dwi_27755.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/03_2024/8dwi_27755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/03_2024/8dwi_27755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/03_2024/8dwi_27755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/03_2024/8dwi_27755.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/03_2024/8dwi_27755.pdb" } resolution = 3.4 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= 0.002 sd= 0.018 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 14 5.16 5 C 2138 2.51 5 N 504 2.21 5 O 536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3192 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3192 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 71 Time building chain proxies: 2.35, per 1000 atoms: 0.74 Number of scatterers: 3192 At special positions: 0 Unit cell: (71.38, 70.55, 72.21, 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 14 16.00 O 536 8.00 N 504 7.00 C 2138 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: 1.32 Conformation dependent library (CDL) restraints added in 593.3 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 38 through 67 removed outlier: 4.163A pdb=" N PHE A 47 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR A 54 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN A 59 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 60 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 61 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 64 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 133 removed outlier: 4.773A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix removed outlier: 4.502A pdb=" N TYR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 176 through 189 Proline residue: A 180 - end of helix removed outlier: 3.910A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 223 removed outlier: 3.849A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 247 removed outlier: 5.193A pdb=" N PHE A 233 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP A 244 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE A 245 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.981A pdb=" N SER A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.871A pdb=" N GLN A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 382 removed outlier: 4.217A pdb=" N GLY A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 389 through 408 removed outlier: 3.960A pdb=" N PHE A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N CYS A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 removed outlier: 4.321A pdb=" N LEU A 415 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 417 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 435 through 445 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 453 through 477 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' 197 hydrogen bonds defined for protein. 480 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: 0.84 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: 1.23 - 1.34: 938 1.34 - 1.46: 817 1.46 - 1.58: 1515 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3292 Sorted by residual: bond pdb=" N TYR A 117 " pdb=" CA TYR A 117 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N PHE A 115 " pdb=" CA PHE A 115 " ideal model delta sigma weight residual 1.458 1.481 -0.024 1.30e-02 5.92e+03 3.31e+00 bond pdb=" C VAL A 58 " pdb=" O VAL A 58 " ideal model delta sigma weight residual 1.242 1.230 0.012 1.13e-02 7.83e+03 1.22e+00 bond pdb=" C LEU A 214 " pdb=" N PRO A 215 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.18e+00 bond pdb=" C PHE A 115 " pdb=" N PHE A 116 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.43e-02 4.89e+03 9.67e-01 ... (remaining 3287 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.22: 108 107.22 - 113.91: 1864 113.91 - 120.60: 1388 120.60 - 127.28: 1096 127.28 - 133.97: 51 Bond angle restraints: 4507 Sorted by residual: angle pdb=" N ILE A 435 " pdb=" CA ILE A 435 " pdb=" C ILE A 435 " ideal model delta sigma weight residual 112.61 107.45 5.16 1.45e+00 4.76e-01 1.27e+01 angle pdb=" N PHE A 115 " pdb=" CA PHE A 115 " pdb=" C PHE A 115 " ideal model delta sigma weight residual 112.38 108.50 3.88 1.22e+00 6.72e-01 1.01e+01 angle pdb=" C LYS A 256 " pdb=" N ARG A 257 " pdb=" CA ARG A 257 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.71e+00 angle pdb=" N PHE A 116 " pdb=" CA PHE A 116 " pdb=" C PHE A 116 " ideal model delta sigma weight residual 111.69 107.87 3.82 1.23e+00 6.61e-01 9.63e+00 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 113.07 109.28 3.79 1.36e+00 5.41e-01 7.75e+00 ... (remaining 4502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 1648 15.49 - 30.97: 142 30.97 - 46.46: 43 46.46 - 61.95: 3 61.95 - 77.44: 2 Dihedral angle restraints: 1838 sinusoidal: 627 harmonic: 1211 Sorted by residual: dihedral pdb=" CA LEU A 170 " pdb=" C LEU A 170 " pdb=" N GLU A 171 " pdb=" CA GLU A 171 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LYS A 445 " pdb=" C LYS A 445 " pdb=" N SER A 446 " pdb=" CA SER A 446 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ALA A 382 " pdb=" C ALA A 382 " pdb=" N GLY A 383 " pdb=" CA GLY A 383 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 278 0.027 - 0.054: 148 0.054 - 0.082: 58 0.082 - 0.109: 32 0.109 - 0.136: 5 Chirality restraints: 521 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 -2.49 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PHE A 115 " pdb=" N PHE A 115 " pdb=" C PHE A 115 " pdb=" CB PHE A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA TRP A 186 " pdb=" N TRP A 186 " pdb=" C TRP A 186 " pdb=" CB TRP A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 518 not shown) Planarity restraints: 547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 435 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO A 436 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 163 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 375 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.032 5.00e-02 4.00e+02 ... (remaining 544 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 816 2.79 - 3.32: 3337 3.32 - 3.84: 5401 3.84 - 4.37: 6043 4.37 - 4.90: 10257 Nonbonded interactions: 25854 Sorted by model distance: nonbonded pdb=" OG1 THR A 304 " pdb=" OD1 ASN A 467 " model vdw 2.258 2.440 nonbonded pdb=" N ASP A 104 " pdb=" OD1 ASP A 104 " model vdw 2.447 2.520 nonbonded pdb=" O ALA A 46 " pdb=" N PHE A 50 " model vdw 2.517 2.520 nonbonded pdb=" O PHE A 116 " pdb=" N GLY A 118 " model vdw 2.524 2.520 nonbonded pdb=" O ASN A 323 " pdb=" N ASN A 327 " model vdw 2.545 2.520 ... (remaining 25849 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: 1.460 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: 6.670 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.950 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3203 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 : 0.003 0.032 3292 Z= 0.208 Angle : 0.629 6.398 4507 Z= 0.365 Chirality : 0.042 0.136 521 Planarity : 0.006 0.075 547 Dihedral : 13.015 77.435 1066 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.29 (0.43), residues: 420 helix: 0.78 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -1.77 (0.61), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 246 HIS 0.007 0.001 HIS A 414 PHE 0.016 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.322 Fit side-chains REVERT: A 230 PHE cc_start: 0.4985 (m-80) cc_final: 0.4557 (m-10) REVERT: A 244 TRP cc_start: 0.3185 (t60) cc_final: 0.2467 (t60) REVERT: A 247 LEU cc_start: 0.6669 (mt) cc_final: 0.6219 (pp) REVERT: A 342 MET cc_start: 0.5783 (ttm) cc_final: 0.5446 (mtm) REVERT: A 432 PHE cc_start: 0.3628 (m-80) cc_final: 0.2892 (m-10) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1649 time to fit residues: 11.2716 Evaluate side-chains 34 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 207 GLN A 430 ASN A 488 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5088 moved from start: 0.6748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 3292 Z= 0.420 Angle : 0.922 9.680 4507 Z= 0.490 Chirality : 0.054 0.213 521 Planarity : 0.009 0.075 547 Dihedral : 6.020 20.161 448 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.78 % Allowed : 13.69 % Favored : 81.53 % 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: -2.03 (0.38), residues: 420 helix: -0.99 (0.27), residues: 322 sheet: None (None), residues: 0 loop : -1.99 (0.58), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 103 HIS 0.010 0.004 HIS A 255 PHE 0.046 0.005 PHE A 116 TYR 0.018 0.003 TYR A 421 ARG 0.011 0.002 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 244 TRP cc_start: 0.4636 (t60) cc_final: 0.3756 (t60) REVERT: A 247 LEU cc_start: 0.7309 (mt) cc_final: 0.6636 (pp) REVERT: A 438 MET cc_start: 0.6605 (tmm) cc_final: 0.5985 (mtp) outliers start: 15 outliers final: 6 residues processed: 60 average time/residue: 0.1395 time to fit residues: 10.4920 Evaluate side-chains 42 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 484 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.0010 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 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 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5292 moved from start: 0.7917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3292 Z= 0.227 Angle : 0.605 5.996 4507 Z= 0.314 Chirality : 0.043 0.178 521 Planarity : 0.006 0.055 547 Dihedral : 5.026 22.856 448 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.87 % Allowed : 20.06 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.40), residues: 420 helix: 0.00 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.89 (0.57), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 186 HIS 0.004 0.001 HIS A 414 PHE 0.020 0.002 PHE A 115 TYR 0.011 0.001 TYR A 306 ARG 0.007 0.001 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.6357 (t80) outliers start: 9 outliers final: 4 residues processed: 51 average time/residue: 0.1248 time to fit residues: 8.2318 Evaluate side-chains 41 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 452 THR 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: 0.0060 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5533 moved from start: 0.9166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3292 Z= 0.196 Angle : 0.600 5.554 4507 Z= 0.308 Chirality : 0.042 0.210 521 Planarity : 0.006 0.060 547 Dihedral : 4.863 21.546 448 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.46 % Allowed : 20.06 % Favored : 75.48 % 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: -0.39 (0.40), residues: 420 helix: 0.34 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -2.04 (0.55), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 226 HIS 0.007 0.002 HIS A 183 PHE 0.012 0.001 PHE A 299 TYR 0.019 0.001 TYR A 117 ARG 0.015 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.7134 (tp) cc_final: 0.6843 (tp) REVERT: A 203 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.6309 (t80) REVERT: A 226 TRP cc_start: 0.6404 (p-90) cc_final: 0.6123 (p-90) outliers start: 14 outliers final: 10 residues processed: 49 average time/residue: 0.1306 time to fit residues: 8.2775 Evaluate side-chains 48 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 484 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 10 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 1.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3292 Z= 0.235 Angle : 0.627 6.233 4507 Z= 0.333 Chirality : 0.042 0.145 521 Planarity : 0.006 0.060 547 Dihedral : 4.784 20.844 448 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.41 % Allowed : 22.93 % Favored : 71.66 % 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: -0.62 (0.40), residues: 420 helix: 0.22 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -2.28 (0.52), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 186 HIS 0.006 0.001 HIS A 414 PHE 0.013 0.002 PHE A 299 TYR 0.019 0.001 TYR A 117 ARG 0.010 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7788 (tp30) cc_final: 0.7554 (tp30) REVERT: A 203 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6764 (t80) outliers start: 17 outliers final: 7 residues processed: 62 average time/residue: 0.1186 time to fit residues: 9.5422 Evaluate side-chains 50 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.0050 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 1.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3292 Z= 0.231 Angle : 0.643 7.694 4507 Z= 0.316 Chirality : 0.042 0.238 521 Planarity : 0.006 0.064 547 Dihedral : 4.918 21.996 448 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.55 % Allowed : 27.39 % Favored : 70.06 % 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: -0.38 (0.41), residues: 420 helix: 0.41 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.20 (0.53), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 244 HIS 0.007 0.001 HIS A 414 PHE 0.027 0.002 PHE A 115 TYR 0.006 0.001 TYR A 203 ARG 0.012 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.335 Fit side-chains REVERT: A 110 TRP cc_start: 0.7686 (m100) cc_final: 0.7364 (m100) REVERT: A 167 LEU cc_start: 0.7190 (tp) cc_final: 0.6965 (tp) REVERT: A 203 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.6877 (t80) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.1278 time to fit residues: 8.0950 Evaluate side-chains 45 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.0470 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 1.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3292 Z= 0.211 Angle : 0.671 14.988 4507 Z= 0.321 Chirality : 0.042 0.148 521 Planarity : 0.005 0.060 547 Dihedral : 4.823 18.194 448 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.50 % Allowed : 28.03 % Favored : 68.47 % 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: -0.48 (0.41), residues: 420 helix: 0.39 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.30 (0.50), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 189 HIS 0.004 0.001 HIS A 414 PHE 0.023 0.002 PHE A 115 TYR 0.007 0.001 TYR A 203 ARG 0.006 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.292 Fit side-chains REVERT: A 110 TRP cc_start: 0.7727 (m100) cc_final: 0.7384 (m100) REVERT: A 137 MET cc_start: 0.6928 (mpp) cc_final: 0.6605 (mmt) REVERT: A 167 LEU cc_start: 0.7213 (tp) cc_final: 0.6969 (tp) REVERT: A 203 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6683 (t80) outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 0.1101 time to fit residues: 7.8462 Evaluate side-chains 49 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 1.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3292 Z= 0.309 Angle : 0.804 14.269 4507 Z= 0.394 Chirality : 0.045 0.151 521 Planarity : 0.006 0.058 547 Dihedral : 5.376 20.768 448 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.14 % Allowed : 27.39 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.40), residues: 420 helix: -0.04 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -2.21 (0.51), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 240 HIS 0.006 0.002 HIS A 414 PHE 0.024 0.002 PHE A 115 TYR 0.016 0.002 TYR A 128 ARG 0.014 0.002 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.345 Fit side-chains REVERT: A 128 TYR cc_start: 0.7499 (t80) cc_final: 0.6314 (m-10) REVERT: A 137 MET cc_start: 0.7215 (mpp) cc_final: 0.6840 (mmt) REVERT: A 203 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.6896 (t80) REVERT: A 284 PRO cc_start: 0.6672 (Cg_exo) cc_final: 0.6380 (Cg_endo) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 0.1196 time to fit residues: 10.8577 Evaluate side-chains 61 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 292 TRP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 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 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 1.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3292 Z= 0.231 Angle : 0.683 9.930 4507 Z= 0.331 Chirality : 0.043 0.126 521 Planarity : 0.006 0.059 547 Dihedral : 5.000 19.870 448 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.23 % Allowed : 30.57 % Favored : 67.20 % 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: -0.58 (0.41), residues: 420 helix: 0.27 (0.31), residues: 309 sheet: None (None), residues: 0 loop : -2.11 (0.51), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 226 HIS 0.012 0.002 HIS A 414 PHE 0.020 0.002 PHE A 115 TYR 0.023 0.001 TYR A 203 ARG 0.008 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.357 Fit side-chains REVERT: A 128 TYR cc_start: 0.7659 (t80) cc_final: 0.6655 (m-10) REVERT: A 137 MET cc_start: 0.7053 (mpp) cc_final: 0.6795 (mmt) REVERT: A 203 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.6407 (t80) REVERT: A 284 PRO cc_start: 0.6974 (Cg_exo) cc_final: 0.6753 (Cg_endo) REVERT: A 438 MET cc_start: 0.7881 (mtm) cc_final: 0.7462 (mtm) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.1132 time to fit residues: 8.7833 Evaluate side-chains 56 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.0970 chunk 30 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 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 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 1.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3292 Z= 0.214 Angle : 0.660 8.246 4507 Z= 0.327 Chirality : 0.042 0.131 521 Planarity : 0.005 0.059 547 Dihedral : 4.893 18.169 448 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.91 % Allowed : 32.17 % Favored : 65.92 % 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: -0.43 (0.41), residues: 420 helix: 0.36 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -2.07 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 226 HIS 0.012 0.002 HIS A 414 PHE 0.019 0.002 PHE A 115 TYR 0.019 0.001 TYR A 203 ARG 0.008 0.001 ARG A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.337 Fit side-chains REVERT: A 128 TYR cc_start: 0.7514 (t80) cc_final: 0.6633 (m-10) REVERT: A 182 MET cc_start: 0.6556 (tmm) cc_final: 0.6176 (tmm) REVERT: A 203 TYR cc_start: 0.6354 (OUTLIER) cc_final: 0.5877 (t80) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.1203 time to fit residues: 9.7844 Evaluate side-chains 57 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.0010 chunk 22 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** 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 = 0.4572 r_free = 0.4572 target = 0.207886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.171222 restraints weight = 4541.781| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 3.32 r_work: 0.4123 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 1.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3292 Z= 0.201 Angle : 0.690 8.475 4507 Z= 0.333 Chirality : 0.042 0.145 521 Planarity : 0.005 0.057 547 Dihedral : 4.924 22.536 448 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.23 % Allowed : 32.17 % Favored : 65.61 % 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: -0.30 (0.42), residues: 420 helix: 0.47 (0.31), residues: 316 sheet: None (None), residues: 0 loop : -2.13 (0.53), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 226 HIS 0.014 0.002 HIS A 414 PHE 0.018 0.001 PHE A 115 TYR 0.011 0.001 TYR A 203 ARG 0.010 0.001 ARG A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1179.23 seconds wall clock time: 21 minutes 51.92 seconds (1311.92 seconds total)