Starting phenix.real_space_refine on Sun Mar 10 16:22:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gof_34177/03_2024/8gof_34177_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gof_34177/03_2024/8gof_34177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gof_34177/03_2024/8gof_34177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gof_34177/03_2024/8gof_34177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gof_34177/03_2024/8gof_34177_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gof_34177/03_2024/8gof_34177_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 10 5.16 5 C 2192 2.51 5 N 545 2.21 5 O 552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" 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: 3299 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3299 Unusual residues: {'LYA': 1} Classifications: {'peptide': 407, 'undetermined': 1} Link IDs: {'PTRANS': 14, 'TRANS': 392, None: 1} Not linked: pdbres="HIS A 457 " pdbres="LYA A 601 " Chain breaks: 1 Time building chain proxies: 2.55, per 1000 atoms: 0.77 Number of scatterers: 3299 At special positions: 0 Unit cell: (80, 72, 66, 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 10 16.00 O 552 8.00 N 545 7.00 C 2192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 620.3 milliseconds 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 74.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 removed outlier: 3.520A pdb=" N CYS A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR A 31 " --> pdb=" O HIS A 27 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.517A pdb=" N ASN A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 89 removed outlier: 3.587A pdb=" N TYR A 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER A 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 79 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 80 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL A 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.001A pdb=" N THR A 87 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A 89 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 112 removed outlier: 3.524A pdb=" N PHE A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.517A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 143 removed outlier: 3.868A pdb=" N TYR A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.824A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.886A pdb=" N ASP A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.558A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 306 through 326 removed outlier: 3.698A pdb=" N THR A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 354 removed outlier: 3.549A pdb=" N THR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 387 removed outlier: 3.670A pdb=" N ILE A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TRP A 363 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 366 " --> pdb=" O TRP A 363 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 368 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 370 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU A 371 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 374 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN A 377 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 378 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 380 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 3.848A pdb=" N THR A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 385 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 386 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 387 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 417 removed outlier: 3.520A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 452 removed outlier: 3.504A pdb=" N GLN A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 498 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: 0.72 Time building geometry restraints manager: 1.45 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: 987 1.34 - 1.46: 765 1.46 - 1.57: 1623 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3391 Sorted by residual: bond pdb=" N MET A 130 " pdb=" CA MET A 130 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.04e+00 bond pdb=" C12 LYA A 601 " pdb=" N11 LYA A 601 " ideal model delta sigma weight residual 1.340 1.370 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C10 LYA A 601 " pdb=" N11 LYA A 601 " ideal model delta sigma weight residual 1.384 1.355 0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C VAL A 81 " pdb=" O VAL A 81 " ideal model delta sigma weight residual 1.240 1.223 0.017 1.26e-02 6.30e+03 1.82e+00 bond pdb=" C17 LYA A 601 " pdb=" N16 LYA A 601 " ideal model delta sigma weight residual 1.305 1.331 -0.026 2.00e-02 2.50e+03 1.72e+00 ... (remaining 3386 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.57: 55 105.57 - 112.84: 1783 112.84 - 120.12: 1390 120.12 - 127.39: 1355 127.39 - 134.66: 39 Bond angle restraints: 4622 Sorted by residual: angle pdb=" N PHE A 103 " pdb=" CA PHE A 103 " pdb=" C PHE A 103 " ideal model delta sigma weight residual 111.40 105.48 5.92 1.22e+00 6.72e-01 2.35e+01 angle pdb=" C TYR A 92 " pdb=" CA TYR A 92 " pdb=" CB TYR A 92 " ideal model delta sigma weight residual 110.42 102.32 8.10 1.99e+00 2.53e-01 1.66e+01 angle pdb=" N LEU A 162 " pdb=" CA LEU A 162 " pdb=" C LEU A 162 " ideal model delta sigma weight residual 112.23 107.69 4.54 1.26e+00 6.30e-01 1.30e+01 angle pdb=" N ILE A 329 " pdb=" CA ILE A 329 " pdb=" C ILE A 329 " ideal model delta sigma weight residual 112.96 109.62 3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" N VAL A 428 " pdb=" CA VAL A 428 " pdb=" C VAL A 428 " ideal model delta sigma weight residual 111.17 115.69 -4.52 1.38e+00 5.25e-01 1.07e+01 ... (remaining 4617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 1772 16.07 - 32.13: 132 32.13 - 48.19: 31 48.19 - 64.26: 11 64.26 - 80.32: 2 Dihedral angle restraints: 1948 sinusoidal: 750 harmonic: 1198 Sorted by residual: dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CB ARG A 373 " pdb=" CG ARG A 373 " pdb=" CD ARG A 373 " pdb=" NE ARG A 373 " ideal model delta sinusoidal sigma weight residual 60.00 118.74 -58.74 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA VAL A 418 " pdb=" C VAL A 418 " pdb=" N SER A 419 " pdb=" CA SER A 419 " ideal model delta harmonic sigma weight residual 180.00 -164.62 -15.38 0 5.00e+00 4.00e-02 9.46e+00 ... (remaining 1945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 343 0.041 - 0.081: 157 0.081 - 0.122: 26 0.122 - 0.163: 7 0.163 - 0.203: 1 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ARG A 42 " pdb=" N ARG A 42 " pdb=" C ARG A 42 " pdb=" CB ARG A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA LYS A 57 " pdb=" N LYS A 57 " pdb=" C LYS A 57 " pdb=" CB LYS A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 531 not shown) Planarity restraints: 559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 LYA A 601 " -0.041 2.00e-02 2.50e+03 1.04e-01 1.36e+02 pdb=" C23 LYA A 601 " 0.127 2.00e-02 2.50e+03 pdb=" C4 LYA A 601 " 0.097 2.00e-02 2.50e+03 pdb=" N22 LYA A 601 " -0.163 2.00e-02 2.50e+03 pdb=" O21 LYA A 601 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.044 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO A 70 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 41 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C ILE A 41 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE A 41 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 42 " 0.013 2.00e-02 2.50e+03 ... (remaining 556 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 991 2.79 - 3.32: 2962 3.32 - 3.85: 5677 3.85 - 4.37: 7168 4.37 - 4.90: 11662 Nonbonded interactions: 28460 Sorted by model distance: nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.269 2.440 nonbonded pdb=" OD1 ASP A 88 " pdb=" OH TYR A 92 " model vdw 2.271 2.440 nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.278 2.440 nonbonded pdb=" O LEU A 32 " pdb=" OH TYR A 136 " model vdw 2.298 2.440 nonbonded pdb=" O VAL A 380 " pdb=" OG1 THR A 384 " model vdw 2.324 2.440 ... (remaining 28455 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.220 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.530 Find NCS groups from input model: 0.070 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.006 0.056 3391 Z= 0.387 Angle : 0.799 8.103 4622 Z= 0.453 Chirality : 0.046 0.203 534 Planarity : 0.007 0.104 559 Dihedral : 13.255 80.321 1178 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % 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: -6.52 (0.22), residues: 403 helix: -4.45 (0.11), residues: 322 sheet: None (None), residues: 0 loop : -2.16 (0.54), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 107 HIS 0.002 0.001 HIS A 114 PHE 0.016 0.002 PHE A 37 TYR 0.011 0.002 TYR A 92 ARG 0.003 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.380 Fit side-chains REVERT: A 60 THR cc_start: 0.8565 (m) cc_final: 0.8328 (p) REVERT: A 277 ASN cc_start: 0.8309 (t0) cc_final: 0.7975 (t160) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 1.4457 time to fit residues: 60.9686 Evaluate side-chains 29 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 293 ASN A 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3391 Z= 0.199 Angle : 0.512 5.537 4622 Z= 0.272 Chirality : 0.038 0.118 534 Planarity : 0.005 0.037 559 Dihedral : 7.560 89.183 469 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.42 % Allowed : 11.68 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.33), residues: 403 helix: -2.10 (0.22), residues: 320 sheet: None (None), residues: 0 loop : -1.60 (0.55), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.010 0.001 PHE A 351 TYR 0.012 0.001 TYR A 35 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.385 Fit side-chains REVERT: A 204 LYS cc_start: 0.7802 (tttm) cc_final: 0.7488 (tttm) REVERT: A 251 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7967 (mm) REVERT: A 277 ASN cc_start: 0.8485 (t160) cc_final: 0.8109 (t160) REVERT: A 358 HIS cc_start: 0.7590 (t-90) cc_final: 0.7346 (t-170) outliers start: 5 outliers final: 0 residues processed: 43 average time/residue: 1.2357 time to fit residues: 54.9049 Evaluate side-chains 37 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3391 Z= 0.196 Angle : 0.467 5.445 4622 Z= 0.245 Chirality : 0.037 0.115 534 Planarity : 0.004 0.030 559 Dihedral : 6.931 84.139 469 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.71 % Allowed : 13.68 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.38), residues: 403 helix: -0.55 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.33 (0.57), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.006 0.001 PHE A 276 TYR 0.012 0.001 TYR A 35 ARG 0.004 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.360 Fit side-chains REVERT: A 45 GLU cc_start: 0.7828 (tt0) cc_final: 0.7216 (tt0) REVERT: A 204 LYS cc_start: 0.7819 (tttm) cc_final: 0.7481 (tttm) REVERT: A 251 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7764 (mm) REVERT: A 277 ASN cc_start: 0.8502 (t160) cc_final: 0.8115 (t160) REVERT: A 293 ASN cc_start: 0.8697 (t0) cc_final: 0.8329 (t0) REVERT: A 358 HIS cc_start: 0.7535 (t-90) cc_final: 0.7293 (t-170) REVERT: A 393 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8325 (tppp) outliers start: 6 outliers final: 0 residues processed: 39 average time/residue: 1.3215 time to fit residues: 53.2126 Evaluate side-chains 37 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 393 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3391 Z= 0.157 Angle : 0.437 5.312 4622 Z= 0.228 Chirality : 0.036 0.114 534 Planarity : 0.003 0.026 559 Dihedral : 6.169 72.811 469 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.99 % Allowed : 15.10 % Favored : 82.91 % 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: -0.09 (0.40), residues: 403 helix: 0.30 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -1.09 (0.57), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.006 0.001 PHE A 276 TYR 0.010 0.001 TYR A 136 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.377 Fit side-chains REVERT: A 45 GLU cc_start: 0.7745 (tt0) cc_final: 0.7140 (tt0) REVERT: A 162 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7515 (tt) REVERT: A 251 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7690 (mm) REVERT: A 277 ASN cc_start: 0.8519 (t160) cc_final: 0.8118 (t160) REVERT: A 393 LYS cc_start: 0.8520 (tppt) cc_final: 0.8305 (tppp) outliers start: 7 outliers final: 0 residues processed: 41 average time/residue: 1.2095 time to fit residues: 51.3340 Evaluate side-chains 34 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3391 Z= 0.235 Angle : 0.474 5.336 4622 Z= 0.245 Chirality : 0.039 0.119 534 Planarity : 0.003 0.028 559 Dihedral : 6.226 72.321 469 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.99 % Allowed : 14.25 % Favored : 83.76 % 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: 0.27 (0.41), residues: 403 helix: 0.55 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.92 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.007 0.001 PHE A 276 TYR 0.013 0.001 TYR A 35 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.382 Fit side-chains REVERT: A 45 GLU cc_start: 0.7780 (tt0) cc_final: 0.7166 (tt0) REVERT: A 162 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7531 (tt) REVERT: A 204 LYS cc_start: 0.7852 (tttm) cc_final: 0.7451 (tttm) REVERT: A 251 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7739 (mm) REVERT: A 277 ASN cc_start: 0.8436 (t160) cc_final: 0.8147 (t160) REVERT: A 393 LYS cc_start: 0.8539 (tppt) cc_final: 0.8317 (tppp) outliers start: 7 outliers final: 2 residues processed: 41 average time/residue: 1.3817 time to fit residues: 58.3338 Evaluate side-chains 38 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 358 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 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 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3391 Z= 0.180 Angle : 0.446 5.252 4622 Z= 0.232 Chirality : 0.037 0.115 534 Planarity : 0.003 0.027 559 Dihedral : 6.017 68.573 469 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.28 % Allowed : 14.81 % Favored : 82.91 % 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: 0.61 (0.42), residues: 403 helix: 0.80 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.85 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.006 0.001 PHE A 276 TYR 0.011 0.001 TYR A 35 ARG 0.006 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.456 Fit side-chains REVERT: A 45 GLU cc_start: 0.7755 (tt0) cc_final: 0.7105 (tt0) REVERT: A 162 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7509 (tt) REVERT: A 204 LYS cc_start: 0.7930 (tttm) cc_final: 0.7579 (tttm) REVERT: A 277 ASN cc_start: 0.8433 (t160) cc_final: 0.8121 (t160) REVERT: A 393 LYS cc_start: 0.8487 (tppt) cc_final: 0.8277 (tppp) outliers start: 8 outliers final: 3 residues processed: 42 average time/residue: 1.2734 time to fit residues: 55.2359 Evaluate side-chains 38 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 358 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3391 Z= 0.193 Angle : 0.452 5.250 4622 Z= 0.234 Chirality : 0.038 0.117 534 Planarity : 0.003 0.027 559 Dihedral : 6.159 72.698 469 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.42 % Allowed : 15.95 % Favored : 82.62 % 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: 0.81 (0.42), residues: 403 helix: 0.94 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.78 (0.60), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.006 0.001 PHE A 276 TYR 0.011 0.001 TYR A 35 ARG 0.006 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.389 Fit side-chains REVERT: A 45 GLU cc_start: 0.7763 (tt0) cc_final: 0.7111 (tt0) REVERT: A 204 LYS cc_start: 0.7930 (tttm) cc_final: 0.7562 (tttm) REVERT: A 277 ASN cc_start: 0.8441 (t160) cc_final: 0.8121 (t160) REVERT: A 393 LYS cc_start: 0.8510 (tppt) cc_final: 0.8299 (tppp) outliers start: 5 outliers final: 1 residues processed: 40 average time/residue: 1.2533 time to fit residues: 51.7719 Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3391 Z= 0.205 Angle : 0.457 5.258 4622 Z= 0.236 Chirality : 0.038 0.117 534 Planarity : 0.003 0.027 559 Dihedral : 6.253 74.363 469 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.71 % Allowed : 15.67 % Favored : 82.62 % 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: 0.94 (0.42), residues: 403 helix: 1.03 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.73 (0.61), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.006 0.001 PHE A 276 TYR 0.011 0.001 TYR A 35 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.396 Fit side-chains REVERT: A 26 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.5897 (mmt180) REVERT: A 45 GLU cc_start: 0.7767 (tt0) cc_final: 0.7115 (tt0) REVERT: A 204 LYS cc_start: 0.7952 (tttm) cc_final: 0.7541 (tttm) outliers start: 6 outliers final: 1 residues processed: 38 average time/residue: 1.4092 time to fit residues: 55.2681 Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 161 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3391 Z= 0.165 Angle : 0.440 5.200 4622 Z= 0.228 Chirality : 0.037 0.114 534 Planarity : 0.003 0.026 559 Dihedral : 6.029 70.463 469 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.85 % Allowed : 16.52 % Favored : 82.62 % 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: 1.17 (0.42), residues: 403 helix: 1.22 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.74 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.005 0.001 PHE A 276 TYR 0.010 0.001 TYR A 35 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.375 Fit side-chains REVERT: A 26 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.5937 (mmt180) REVERT: A 45 GLU cc_start: 0.7731 (tt0) cc_final: 0.7092 (tt0) outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 1.3859 time to fit residues: 51.4922 Evaluate side-chains 36 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3391 Z= 0.190 Angle : 0.450 5.242 4622 Z= 0.233 Chirality : 0.038 0.116 534 Planarity : 0.003 0.027 559 Dihedral : 5.999 68.723 469 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.57 % Allowed : 16.81 % Favored : 82.62 % 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: 1.19 (0.42), residues: 403 helix: 1.24 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.74 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.006 0.001 PHE A 276 TYR 0.010 0.001 TYR A 35 ARG 0.005 0.000 ARG A 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.567 Fit side-chains REVERT: A 26 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.5901 (mmt180) REVERT: A 45 GLU cc_start: 0.7704 (tt0) cc_final: 0.7085 (tt0) outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 1.3716 time to fit residues: 48.1500 Evaluate side-chains 35 residues out of total 351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.087696 restraints weight = 4120.475| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.64 r_work: 0.2828 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3391 Z= 0.214 Angle : 0.462 5.263 4622 Z= 0.238 Chirality : 0.038 0.118 534 Planarity : 0.003 0.027 559 Dihedral : 6.070 68.949 469 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.85 % Allowed : 16.52 % Favored : 82.62 % 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: 1.15 (0.42), residues: 403 helix: 1.20 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.73 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.006 0.001 PHE A 276 TYR 0.012 0.001 TYR A 35 ARG 0.005 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1613.46 seconds wall clock time: 29 minutes 28.54 seconds (1768.54 seconds total)