Starting phenix.real_space_refine on Sun Mar 10 15:44:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/03_2024/8ctd_26986.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/03_2024/8ctd_26986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/03_2024/8ctd_26986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/03_2024/8ctd_26986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/03_2024/8ctd_26986.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/03_2024/8ctd_26986.pdb" } resolution = 3.42 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= 0.006 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: 6 Type Number sf(0) Gaussians Hg 1 10.96 5 S 20 5.16 5 Na 3 4.78 5 C 2051 2.51 5 N 498 2.21 5 O 557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 208": "OD1" <-> "OD2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 600": "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: 3130 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3130 Unusual residues: {' HG': 1, ' NA': 3} Inner-chain residues flagged as termini: ['pdbres="GLU A 600 "'] Classifications: {'peptide': 411, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 399, None: 4} Not linked: pdbres="GLU A 600 " pdbres=" NA A 601 " Not linked: pdbres=" NA A 601 " pdbres=" NA A 602 " Not linked: pdbres=" NA A 602 " pdbres=" NA A 603 " Not linked: pdbres=" NA A 603 " pdbres=" HG A 604 " Chain breaks: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1608 SG CYS A 269 46.477 24.191 27.992 1.00 77.16 S ATOM 2889 SG CYS A 441 42.130 25.493 25.757 1.00158.28 S Time building chain proxies: 2.37, per 1000 atoms: 0.76 Number of scatterers: 3130 At special positions: 0 Unit cell: (71.478, 66.063, 76.893, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 1 79.96 S 20 16.00 Na 3 11.00 O 557 8.00 N 498 7.00 C 2051 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: 1.33 Conformation dependent library (CDL) restraints added in 631.7 milliseconds 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 1 sheets defined 83.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.836A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.655A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.678A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.831A pdb=" N ILE A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 117 removed outlier: 3.840A pdb=" N LYS A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 removed outlier: 4.408A pdb=" N THR A 121 " --> pdb=" O PRO A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 118 through 121' Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.639A pdb=" N LEU A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.586A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 212 through 230 Processing helix chain 'A' and resid 233 through 272 removed outlier: 3.598A pdb=" N PHE A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.897A pdb=" N ARG A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 4.365A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.785A pdb=" N LEU A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 removed outlier: 4.165A pdb=" N GLU A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.911A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 removed outlier: 3.612A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 removed outlier: 3.719A pdb=" N CYS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 466 removed outlier: 4.134A pdb=" N ASN A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 224 hydrogen bonds defined for protein. 666 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: 0.76 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 581 1.33 - 1.45: 675 1.45 - 1.57: 1878 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 3171 Sorted by residual: bond pdb=" N ILE A 436 " pdb=" CA ILE A 436 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.59e+00 bond pdb=" N ILE A 437 " pdb=" CA ILE A 437 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.43e+00 bond pdb=" N VAL A 439 " pdb=" CA VAL A 439 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.37e-02 5.33e+03 6.92e+00 bond pdb=" N ASP A 351 " pdb=" CA ASP A 351 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.67e+00 bond pdb=" N ASP A 440 " pdb=" CA ASP A 440 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.21e-02 6.83e+03 6.33e+00 ... (remaining 3166 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.87: 64 106.87 - 113.63: 1858 113.63 - 120.40: 1226 120.40 - 127.16: 1137 127.16 - 133.93: 19 Bond angle restraints: 4304 Sorted by residual: angle pdb=" N VAL A 439 " pdb=" CA VAL A 439 " pdb=" C VAL A 439 " ideal model delta sigma weight residual 112.83 109.40 3.43 9.90e-01 1.02e+00 1.20e+01 angle pdb=" C LYS A 16 " pdb=" N ASN A 17 " pdb=" CA ASN A 17 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C VAL A 411 " pdb=" N PRO A 412 " pdb=" CA PRO A 412 " ideal model delta sigma weight residual 119.56 122.82 -3.26 1.01e+00 9.80e-01 1.04e+01 angle pdb=" CA MET A 449 " pdb=" C MET A 449 " pdb=" O MET A 449 " ideal model delta sigma weight residual 120.82 117.67 3.15 1.05e+00 9.07e-01 8.98e+00 angle pdb=" CA MET A 367 " pdb=" C MET A 367 " pdb=" O MET A 367 " ideal model delta sigma weight residual 121.86 117.92 3.94 1.39e+00 5.18e-01 8.03e+00 ... (remaining 4299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.86: 1585 13.86 - 27.72: 203 27.72 - 41.57: 82 41.57 - 55.43: 20 55.43 - 69.29: 5 Dihedral angle restraints: 1895 sinusoidal: 718 harmonic: 1177 Sorted by residual: dihedral pdb=" CA ARG A 61 " pdb=" CB ARG A 61 " pdb=" CG ARG A 61 " pdb=" CD ARG A 61 " ideal model delta sinusoidal sigma weight residual -60.00 -119.48 59.48 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 229 " pdb=" CG MET A 229 " pdb=" SD MET A 229 " pdb=" CE MET A 229 " ideal model delta sinusoidal sigma weight residual 60.00 1.97 58.03 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LEU A 325 " pdb=" CA LEU A 325 " pdb=" CB LEU A 325 " pdb=" CG LEU A 325 " ideal model delta sinusoidal sigma weight residual -60.00 -115.89 55.89 3 1.50e+01 4.44e-03 9.37e+00 ... (remaining 1892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 388 0.040 - 0.081: 122 0.081 - 0.121: 27 0.121 - 0.161: 11 0.161 - 0.202: 1 Chirality restraints: 549 Sorted by residual: chirality pdb=" CA MET A 367 " pdb=" N MET A 367 " pdb=" C MET A 367 " pdb=" CB MET A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LYS A 117 " pdb=" N LYS A 117 " pdb=" C LYS A 117 " pdb=" CB LYS A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA ILE A 436 " pdb=" N ILE A 436 " pdb=" C ILE A 436 " pdb=" CB ILE A 436 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 546 not shown) Planarity restraints: 523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 258 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO A 259 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 434 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C THR A 434 " -0.035 2.00e-02 2.50e+03 pdb=" O THR A 434 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 435 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 373 " -0.004 2.00e-02 2.50e+03 9.03e-03 1.63e+00 pdb=" CG TYR A 373 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 373 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 373 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 373 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 373 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 373 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 373 " 0.002 2.00e-02 2.50e+03 ... (remaining 520 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 660 2.78 - 3.31: 3212 3.31 - 3.84: 5069 3.84 - 4.37: 5614 4.37 - 4.90: 9944 Nonbonded interactions: 24499 Sorted by model distance: nonbonded pdb=" OG1 THR A 101 " pdb="NA NA A 603 " model vdw 2.248 2.470 nonbonded pdb=" O ASP A 444 " pdb=" OD1 ASP A 444 " model vdw 2.266 3.040 nonbonded pdb=" SG CYS A 441 " pdb="HG HG A 604 " model vdw 2.291 2.880 nonbonded pdb=" O ALA A 456 " pdb=" OG1 THR A 459 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR A 373 " pdb=" OD1 ASP A 440 " model vdw 2.311 2.440 ... (remaining 24494 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: 0.750 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: 3.650 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.080 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 0.036 3171 Z= 0.225 Angle : 0.630 6.501 4304 Z= 0.398 Chirality : 0.044 0.202 549 Planarity : 0.004 0.056 523 Dihedral : 15.424 69.290 1135 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 22.22 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.44), residues: 404 helix: 1.12 (0.31), residues: 317 sheet: 0.22 (1.19), residues: 18 loop : -1.82 (0.69), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 276 HIS 0.000 0.000 HIS A 41 PHE 0.009 0.001 PHE A 341 TYR 0.021 0.001 TYR A 373 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.339 Fit side-chains REVERT: A 117 LYS cc_start: 0.7208 (pttt) cc_final: 0.6915 (pttp) REVERT: A 286 MET cc_start: 0.7264 (mtp) cc_final: 0.7001 (mtt) REVERT: A 315 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7310 (mtt180) REVERT: A 373 TYR cc_start: 0.6514 (t80) cc_final: 0.5804 (t80) REVERT: A 385 ASN cc_start: 0.6365 (m-40) cc_final: 0.5958 (m-40) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1585 time to fit residues: 14.4358 Evaluate side-chains 63 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 19 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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: 0.7619 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3171 Z= 0.153 Angle : 0.522 7.416 4304 Z= 0.266 Chirality : 0.038 0.133 549 Planarity : 0.004 0.053 523 Dihedral : 3.448 11.284 431 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.22 % Allowed : 21.35 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.45), residues: 404 helix: 1.48 (0.31), residues: 321 sheet: 0.03 (1.16), residues: 18 loop : -1.71 (0.70), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.000 0.000 HIS A 296 PHE 0.016 0.001 PHE A 457 TYR 0.024 0.002 TYR A 97 ARG 0.003 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.387 Fit side-chains REVERT: A 117 LYS cc_start: 0.7594 (pttt) cc_final: 0.7103 (pttp) REVERT: A 258 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8249 (ttp) REVERT: A 373 TYR cc_start: 0.6935 (t80) cc_final: 0.6088 (t80) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 0.1338 time to fit residues: 11.7435 Evaluate side-chains 70 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 30 optimal weight: 0.2980 chunk 25 optimal weight: 0.0770 chunk 10 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.0170 chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.1776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3171 Z= 0.134 Angle : 0.472 6.345 4304 Z= 0.241 Chirality : 0.037 0.129 549 Planarity : 0.004 0.051 523 Dihedral : 3.346 10.612 431 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.80 % Allowed : 21.93 % Favored : 74.27 % 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: 1.73 (0.44), residues: 404 helix: 1.80 (0.31), residues: 316 sheet: -0.08 (1.18), residues: 18 loop : -1.53 (0.66), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 276 HIS 0.000 0.000 HIS A 41 PHE 0.015 0.001 PHE A 457 TYR 0.011 0.001 TYR A 97 ARG 0.001 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.343 Fit side-chains REVERT: A 117 LYS cc_start: 0.7455 (pttt) cc_final: 0.7103 (pttp) REVERT: A 328 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6691 (tt) REVERT: A 373 TYR cc_start: 0.6886 (t80) cc_final: 0.6209 (t80) outliers start: 13 outliers final: 6 residues processed: 73 average time/residue: 0.1420 time to fit residues: 12.8360 Evaluate side-chains 68 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.0470 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.0070 chunk 33 optimal weight: 1.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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: 0.7613 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3171 Z= 0.161 Angle : 0.503 8.203 4304 Z= 0.252 Chirality : 0.037 0.140 549 Planarity : 0.004 0.051 523 Dihedral : 3.387 10.632 431 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.80 % Allowed : 23.10 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.44), residues: 404 helix: 1.78 (0.31), residues: 316 sheet: -0.41 (1.16), residues: 18 loop : -1.52 (0.66), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.011 0.001 PHE A 457 TYR 0.011 0.001 TYR A 97 ARG 0.001 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.341 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 67 average time/residue: 0.1450 time to fit residues: 12.0654 Evaluate side-chains 68 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 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 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3171 Z= 0.175 Angle : 0.511 6.800 4304 Z= 0.257 Chirality : 0.037 0.152 549 Planarity : 0.004 0.054 523 Dihedral : 3.428 10.613 431 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.80 % Allowed : 22.51 % Favored : 73.68 % 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: 1.65 (0.44), residues: 404 helix: 1.75 (0.31), residues: 316 sheet: -0.57 (1.17), residues: 18 loop : -1.45 (0.66), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.000 0.000 HIS A 41 PHE 0.014 0.001 PHE A 341 TYR 0.014 0.001 TYR A 97 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.357 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 69 average time/residue: 0.1477 time to fit residues: 12.7394 Evaluate side-chains 68 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3171 Z= 0.176 Angle : 0.527 9.171 4304 Z= 0.264 Chirality : 0.037 0.147 549 Planarity : 0.004 0.054 523 Dihedral : 3.477 10.809 431 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.09 % Allowed : 22.51 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.44), residues: 404 helix: 1.74 (0.31), residues: 316 sheet: -0.71 (1.14), residues: 18 loop : -1.50 (0.66), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.001 PHE A 457 TYR 0.015 0.001 TYR A 97 ARG 0.001 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.347 Fit side-chains REVERT: A 373 TYR cc_start: 0.6890 (t80) cc_final: 0.6581 (t80) outliers start: 14 outliers final: 10 residues processed: 68 average time/residue: 0.1348 time to fit residues: 11.4345 Evaluate side-chains 70 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.0670 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3171 Z= 0.154 Angle : 0.513 8.449 4304 Z= 0.255 Chirality : 0.037 0.141 549 Planarity : 0.004 0.054 523 Dihedral : 3.429 10.700 431 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.68 % Allowed : 22.22 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.44), residues: 404 helix: 1.79 (0.31), residues: 316 sheet: -0.72 (1.14), residues: 18 loop : -1.53 (0.67), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.019 0.001 PHE A 341 TYR 0.016 0.001 TYR A 97 ARG 0.001 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.374 Fit side-chains REVERT: A 142 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7152 (mmp) REVERT: A 208 ASP cc_start: 0.7506 (t70) cc_final: 0.7236 (t70) REVERT: A 329 MET cc_start: 0.6137 (mmp) cc_final: 0.5764 (mmp) REVERT: A 373 TYR cc_start: 0.6876 (t80) cc_final: 0.6584 (t80) outliers start: 16 outliers final: 9 residues processed: 72 average time/residue: 0.1412 time to fit residues: 12.7130 Evaluate side-chains 73 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3171 Z= 0.189 Angle : 0.533 8.682 4304 Z= 0.267 Chirality : 0.038 0.156 549 Planarity : 0.004 0.054 523 Dihedral : 3.499 10.885 431 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.39 % Allowed : 22.81 % Favored : 72.81 % 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: 1.49 (0.44), residues: 404 helix: 1.65 (0.31), residues: 321 sheet: -0.72 (1.13), residues: 18 loop : -1.79 (0.71), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.017 0.001 PHE A 341 TYR 0.019 0.002 TYR A 97 ARG 0.001 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.361 Fit side-chains REVERT: A 142 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6882 (mmp) REVERT: A 208 ASP cc_start: 0.7507 (t70) cc_final: 0.7228 (t70) REVERT: A 329 MET cc_start: 0.6233 (mmp) cc_final: 0.5864 (mmp) REVERT: A 373 TYR cc_start: 0.6706 (t80) cc_final: 0.6439 (t80) outliers start: 15 outliers final: 13 residues processed: 70 average time/residue: 0.1416 time to fit residues: 12.4400 Evaluate side-chains 75 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3171 Z= 0.150 Angle : 0.534 10.465 4304 Z= 0.262 Chirality : 0.037 0.149 549 Planarity : 0.004 0.054 523 Dihedral : 3.471 10.792 431 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.39 % Allowed : 23.68 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.44), residues: 404 helix: 1.73 (0.31), residues: 316 sheet: -0.81 (1.13), residues: 18 loop : -1.52 (0.68), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.013 0.001 PHE A 457 TYR 0.021 0.002 TYR A 97 ARG 0.001 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.356 Fit side-chains REVERT: A 142 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7027 (mmp) REVERT: A 208 ASP cc_start: 0.7473 (t70) cc_final: 0.7183 (t70) REVERT: A 329 MET cc_start: 0.6196 (mmp) cc_final: 0.5856 (mmp) REVERT: A 373 TYR cc_start: 0.6657 (t80) cc_final: 0.6380 (t80) outliers start: 15 outliers final: 12 residues processed: 68 average time/residue: 0.1344 time to fit residues: 11.3453 Evaluate side-chains 75 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0570 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3171 Z= 0.151 Angle : 0.534 10.295 4304 Z= 0.262 Chirality : 0.037 0.149 549 Planarity : 0.004 0.054 523 Dihedral : 3.457 11.654 431 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.39 % Allowed : 23.39 % Favored : 72.22 % 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: 1.58 (0.44), residues: 404 helix: 1.72 (0.31), residues: 321 sheet: -0.88 (1.13), residues: 18 loop : -1.75 (0.72), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.022 0.001 PHE A 341 TYR 0.024 0.002 TYR A 97 ARG 0.001 0.000 ARG A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.295 Fit side-chains REVERT: A 142 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7029 (mmp) REVERT: A 208 ASP cc_start: 0.7528 (t70) cc_final: 0.7231 (t70) REVERT: A 315 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7468 (mtt180) REVERT: A 329 MET cc_start: 0.6190 (mmp) cc_final: 0.5857 (mmp) outliers start: 15 outliers final: 14 residues processed: 68 average time/residue: 0.1396 time to fit residues: 11.7767 Evaluate side-chains 76 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 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 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.190167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.142251 restraints weight = 2222.657| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.29 r_work: 0.3428 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3171 Z= 0.166 Angle : 0.541 10.346 4304 Z= 0.266 Chirality : 0.037 0.155 549 Planarity : 0.004 0.054 523 Dihedral : 3.499 13.829 431 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.39 % Allowed : 24.27 % Favored : 71.35 % 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: 1.59 (0.45), residues: 404 helix: 1.72 (0.31), residues: 321 sheet: -0.89 (1.13), residues: 18 loop : -1.73 (0.73), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.013 0.001 PHE A 457 TYR 0.022 0.002 TYR A 97 ARG 0.002 0.000 ARG A 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1164.80 seconds wall clock time: 21 minutes 32.56 seconds (1292.56 seconds total)