Starting phenix.real_space_refine on Mon Jul 29 18:56:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/07_2024/8ctd_26986.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/07_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_26986/07_2024/8ctd_26986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/07_2024/8ctd_26986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/07_2024/8ctd_26986.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/07_2024/8ctd_26986.cif" } 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-5388/modules/chem_data/mon_lib" Total number of atoms: 3130 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3126 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 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: 1.62, per 1000 atoms: 0.52 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: 0.83 Conformation dependent library (CDL) restraints added in 363.0 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: 0.21 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: 0.52 Time building geometry restraints manager: 0.90 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: 0.520 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.750 Find NCS groups from input model: 0.020 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:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.120 ------------------------------------------------------------------------------- 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 : 0.209 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: 0.0991 time to fit residues: 9.0111 Evaluate side-chains 63 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 : 0.210 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: 0.0832 time to fit residues: 7.3184 Evaluate side-chains 70 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 0.0070 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.0170 chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 overall best weight: 0.1794 ------------------------------------------------------------------------------- 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: 0.7590 moved from start: 0.1346 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= 0.135 Angle : 0.472 6.292 4304 Z= 0.241 Chirality : 0.037 0.127 549 Planarity : 0.004 0.051 523 Dihedral : 3.355 10.693 431 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.80 % Allowed : 21.64 % Favored : 74.56 % 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: 1.71 (0.44), residues: 404 helix: 1.78 (0.31), residues: 316 sheet: -0.05 (1.18), residues: 18 loop : -1.52 (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 296 PHE 0.014 0.001 PHE A 457 TYR 0.009 0.001 TYR A 97 ARG 0.001 0.000 ARG A 356 *********************** 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 78 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.211 Fit side-chains REVERT: A 117 LYS cc_start: 0.7458 (pttt) cc_final: 0.7101 (pttp) REVERT: A 328 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6695 (tt) REVERT: A 373 TYR cc_start: 0.6879 (t80) cc_final: 0.6212 (t80) outliers start: 13 outliers final: 6 residues processed: 71 average time/residue: 0.0874 time to fit residues: 7.7342 Evaluate side-chains 67 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 167 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR 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: 0.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.7656 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3171 Z= 0.186 Angle : 0.514 8.180 4304 Z= 0.261 Chirality : 0.038 0.146 549 Planarity : 0.004 0.053 523 Dihedral : 3.425 11.489 431 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 1.52 (0.44), residues: 404 helix: 1.65 (0.31), residues: 316 sheet: -0.45 (1.16), residues: 18 loop : -1.49 (0.67), 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 296 PHE 0.011 0.001 PHE A 240 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 76 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.210 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 70 average time/residue: 0.0895 time to fit residues: 7.7825 Evaluate side-chains 69 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 104 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 210 ILE 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=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: 0.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.1980 chunk 10 optimal weight: 0.0770 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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: 0.7630 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3171 Z= 0.155 Angle : 0.503 7.047 4304 Z= 0.252 Chirality : 0.037 0.144 549 Planarity : 0.004 0.053 523 Dihedral : 3.414 10.660 431 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 1.62 (0.44), residues: 404 helix: 1.76 (0.31), residues: 316 sheet: -0.67 (1.15), residues: 18 loop : -1.55 (0.65), 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 296 PHE 0.015 0.001 PHE A 341 TYR 0.013 0.001 TYR A 97 ARG 0.001 0.000 ARG A 39 *********************** 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 79 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.211 Fit side-chains REVERT: A 329 MET cc_start: 0.6181 (mmp) cc_final: 0.5864 (mmp) outliers start: 14 outliers final: 11 residues processed: 71 average time/residue: 0.0835 time to fit residues: 7.4348 Evaluate side-chains 71 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7648 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3171 Z= 0.172 Angle : 0.513 8.603 4304 Z= 0.257 Chirality : 0.037 0.142 549 Planarity : 0.004 0.053 523 Dihedral : 3.429 10.771 431 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.97 % Allowed : 21.35 % 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: 1.54 (0.44), residues: 404 helix: 1.69 (0.31), residues: 316 sheet: -0.71 (1.15), residues: 18 loop : -1.53 (0.65), 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 296 PHE 0.011 0.001 PHE A 457 TYR 0.016 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 76 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.211 Fit side-chains REVERT: A 329 MET cc_start: 0.6028 (mmp) cc_final: 0.5747 (mmp) REVERT: A 373 TYR cc_start: 0.6847 (t80) cc_final: 0.6589 (t80) outliers start: 17 outliers final: 13 residues processed: 69 average time/residue: 0.0841 time to fit residues: 7.2804 Evaluate side-chains 73 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 299 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7652 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3171 Z= 0.170 Angle : 0.529 8.934 4304 Z= 0.262 Chirality : 0.037 0.144 549 Planarity : 0.004 0.054 523 Dihedral : 3.416 10.686 431 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 1.54 (0.44), residues: 404 helix: 1.69 (0.31), residues: 316 sheet: -0.75 (1.15), residues: 18 loop : -1.50 (0.67), 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 0.019 0.001 PHE A 341 TYR 0.018 0.001 TYR A 97 ARG 0.001 0.000 ARG A 342 *********************** 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 78 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.212 Fit side-chains REVERT: A 286 MET cc_start: 0.7079 (mtp) cc_final: 0.6873 (mtp) REVERT: A 329 MET cc_start: 0.6216 (mmp) cc_final: 0.5960 (mmp) REVERT: A 373 TYR cc_start: 0.6802 (t80) cc_final: 0.6522 (t80) outliers start: 16 outliers final: 14 residues processed: 71 average time/residue: 0.0849 time to fit residues: 7.5837 Evaluate side-chains 75 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 299 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 0.0270 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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: 0.7649 moved from start: 0.1860 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= 0.162 Angle : 0.533 9.376 4304 Z= 0.262 Chirality : 0.037 0.146 549 Planarity : 0.004 0.054 523 Dihedral : 3.435 10.790 431 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.68 % Allowed : 23.10 % 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: 1.59 (0.44), residues: 404 helix: 1.72 (0.31), residues: 316 sheet: -0.76 (1.15), residues: 18 loop : -1.50 (0.68), 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 0.017 0.001 PHE A 341 TYR 0.020 0.001 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 78 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.210 Fit side-chains REVERT: A 142 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6877 (mmp) REVERT: A 208 ASP cc_start: 0.7455 (t70) cc_final: 0.7185 (t70) REVERT: A 286 MET cc_start: 0.7093 (mtp) cc_final: 0.6867 (mtp) REVERT: A 329 MET cc_start: 0.6265 (mmp) cc_final: 0.5622 (mmp) REVERT: A 373 TYR cc_start: 0.6778 (t80) cc_final: 0.6526 (t80) outliers start: 16 outliers final: 12 residues processed: 71 average time/residue: 0.0837 time to fit residues: 7.4908 Evaluate side-chains 72 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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: 0.7648 moved from start: 0.1955 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 : 0.535 9.981 4304 Z= 0.265 Chirality : 0.037 0.147 549 Planarity : 0.004 0.054 523 Dihedral : 3.505 13.384 431 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.09 % Allowed : 24.56 % 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 (0.44), residues: 404 helix: 1.76 (0.31), residues: 312 sheet: -0.75 (1.16), residues: 18 loop : -1.51 (0.65), residues: 74 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 0.012 0.001 PHE A 457 TYR 0.022 0.002 TYR A 97 ARG 0.001 0.000 ARG A 342 *********************** 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 76 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.211 Fit side-chains REVERT: A 142 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6876 (mmp) REVERT: A 208 ASP cc_start: 0.7468 (t70) cc_final: 0.7188 (t70) REVERT: A 286 MET cc_start: 0.7094 (mtp) cc_final: 0.6860 (mtp) REVERT: A 329 MET cc_start: 0.6254 (mmp) cc_final: 0.5746 (mmp) outliers start: 14 outliers final: 12 residues processed: 68 average time/residue: 0.0892 time to fit residues: 7.5791 Evaluate side-chains 74 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7668 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3171 Z= 0.185 Angle : 0.554 10.373 4304 Z= 0.275 Chirality : 0.038 0.153 549 Planarity : 0.004 0.054 523 Dihedral : 3.572 12.755 431 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.39 % Allowed : 23.98 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.44), residues: 404 helix: 1.64 (0.31), residues: 317 sheet: -0.78 (1.15), residues: 18 loop : -1.81 (0.68), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.013 0.001 PHE A 341 TYR 0.023 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 78 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.212 Fit side-chains REVERT: A 142 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6921 (mmp) REVERT: A 286 MET cc_start: 0.7168 (mtp) cc_final: 0.6928 (mtp) REVERT: A 329 MET cc_start: 0.6228 (mmp) cc_final: 0.5659 (mmp) outliers start: 15 outliers final: 13 residues processed: 70 average time/residue: 0.0849 time to fit residues: 7.4254 Evaluate side-chains 76 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 299 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.187703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136811 restraints weight = 2236.221| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.36 r_work: 0.3410 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3171 Z= 0.178 Angle : 0.554 10.396 4304 Z= 0.275 Chirality : 0.037 0.150 549 Planarity : 0.004 0.054 523 Dihedral : 3.575 14.011 431 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.91 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: 1.50 (0.44), residues: 404 helix: 1.71 (0.31), residues: 317 sheet: -0.85 (1.14), residues: 18 loop : -1.85 (0.67), residues: 69 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 0.022 0.002 TYR A 97 ARG 0.002 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 747.91 seconds wall clock time: 13 minutes 10.96 seconds (790.96 seconds total)