Starting phenix.real_space_refine on Thu Dec 7 17:09:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/12_2023/8ctd_26986.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/12_2023/8ctd_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_26986/12_2023/8ctd_26986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/12_2023/8ctd_26986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/12_2023/8ctd_26986.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctd_26986/12_2023/8ctd_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-1.21rc1-5172/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: 2.25, per 1000 atoms: 0.72 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: 1.43 Conformation dependent library (CDL) restraints added in 691.2 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: 0.33 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: 0.83 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 0.700 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: 3.670 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.750 Find NCS groups from input model: 0.090 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.230 ------------------------------------------------------------------------------- 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 : 0.316 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1529 time to fit residues: 14.0349 Evaluate side-chains 63 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4636 ------------------------------------------------------------------------------- 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: 9.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 19 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.7629 moved from start: 0.1031 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= 0.167 Angle : 0.529 7.221 4304 Z= 0.270 Chirality : 0.038 0.133 549 Planarity : 0.004 0.053 523 Dihedral : 3.464 11.210 431 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 1.30 (0.44), residues: 404 helix: 1.46 (0.31), residues: 320 sheet: 0.00 (1.16), residues: 18 loop : -1.73 (0.70), residues: 66 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 0.016 0.001 PHE A 457 TYR 0.023 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 78 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.443 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 71 average time/residue: 0.1368 time to fit residues: 12.2295 Evaluate side-chains 71 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0360 time to fit residues: 0.9065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.0040 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.0040 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 0.2004 ------------------------------------------------------------------------------- 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: 0.7592 moved from start: 0.1354 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= 0.139 Angle : 0.477 5.397 4304 Z= 0.246 Chirality : 0.037 0.126 549 Planarity : 0.004 0.051 523 Dihedral : 3.401 10.690 431 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.63 % Allowed : 22.51 % Favored : 74.85 % 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: 1.64 (0.45), residues: 404 helix: 1.73 (0.31), residues: 321 sheet: -0.03 (1.17), residues: 18 loop : -1.81 (0.70), residues: 65 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 0.014 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 74 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.388 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 71 average time/residue: 0.1138 time to fit residues: 10.3138 Evaluate side-chains 62 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0454 time to fit residues: 0.6157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0050 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.0010 chunk 33 optimal weight: 0.6980 overall best weight: 0.4600 ------------------------------------------------------------------------------- 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: 0.1527 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= 0.152 Angle : 0.507 9.058 4304 Z= 0.255 Chirality : 0.037 0.140 549 Planarity : 0.004 0.051 523 Dihedral : 3.390 10.628 431 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.51 % Allowed : 23.39 % 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: 1.74 (0.44), residues: 404 helix: 1.82 (0.31), residues: 321 sheet: -0.34 (1.16), residues: 18 loop : -1.77 (0.69), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 HIS 0.000 0.000 HIS A 296 PHE 0.011 0.001 PHE A 457 TYR 0.012 0.001 TYR A 97 ARG 0.002 0.000 ARG A 447 *********************** 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 79 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.318 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 73 average time/residue: 0.1439 time to fit residues: 12.9520 Evaluate side-chains 65 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0336 time to fit residues: 0.7442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.0470 chunk 27 optimal weight: 0.0770 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.0270 chunk 10 optimal weight: 0.0050 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.1708 ------------------------------------------------------------------------------- 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: 0.7579 moved from start: 0.1718 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= 0.134 Angle : 0.493 7.896 4304 Z= 0.247 Chirality : 0.037 0.131 549 Planarity : 0.004 0.051 523 Dihedral : 3.360 10.693 431 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.05 % Allowed : 24.56 % 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: 1.90 (0.44), residues: 404 helix: 1.95 (0.31), residues: 316 sheet: -0.56 (1.17), residues: 18 loop : -1.50 (0.65), 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 0.013 0.001 PHE A 341 TYR 0.014 0.001 TYR A 97 ARG 0.002 0.000 ARG A 447 *********************** 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 70 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.356 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 67 average time/residue: 0.1327 time to fit residues: 11.2624 Evaluate side-chains 62 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0306 time to fit residues: 0.5942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.0270 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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: 0.7622 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= 0.158 Angle : 0.505 7.453 4304 Z= 0.253 Chirality : 0.037 0.146 549 Planarity : 0.004 0.051 523 Dihedral : 3.350 10.744 431 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.75 % Allowed : 24.27 % Favored : 73.98 % 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: 1.75 (0.44), residues: 404 helix: 1.84 (0.31), residues: 316 sheet: -0.72 (1.16), residues: 18 loop : -1.44 (0.65), 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 0.010 0.001 PHE A 457 TYR 0.014 0.001 TYR A 97 ARG 0.002 0.000 ARG A 447 *********************** 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 72 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.325 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 68 average time/residue: 0.1683 time to fit residues: 13.7332 Evaluate side-chains 64 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0330 time to fit residues: 0.6082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7662 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3171 Z= 0.200 Angle : 0.575 10.383 4304 Z= 0.278 Chirality : 0.038 0.155 549 Planarity : 0.004 0.053 523 Dihedral : 3.444 10.598 431 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.92 % Allowed : 22.51 % 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: 1.60 (0.44), residues: 404 helix: 1.70 (0.31), residues: 321 sheet: -0.72 (1.15), residues: 18 loop : -1.59 (0.70), residues: 65 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 0.016 0.002 TYR A 97 ARG 0.005 0.000 ARG A 447 *********************** 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 73 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.349 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 0.1352 time to fit residues: 11.4937 Evaluate side-chains 65 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0331 time to fit residues: 0.7857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.0010 chunk 37 optimal weight: 0.0040 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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: 0.7632 moved from start: 0.2021 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= 0.155 Angle : 0.551 9.776 4304 Z= 0.266 Chirality : 0.037 0.141 549 Planarity : 0.004 0.053 523 Dihedral : 3.453 10.717 431 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.58 % Allowed : 23.10 % Favored : 76.32 % 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: 1.63 (0.44), residues: 404 helix: 1.72 (0.31), residues: 321 sheet: -0.84 (1.14), residues: 18 loop : -1.53 (0.71), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.017 0.001 PHE A 341 TYR 0.018 0.001 TYR A 97 ARG 0.004 0.000 ARG A 447 *********************** 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 66 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.349 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.1246 time to fit residues: 10.1321 Evaluate side-chains 59 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7641 moved from start: 0.2144 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= 0.167 Angle : 0.565 9.876 4304 Z= 0.273 Chirality : 0.037 0.153 549 Planarity : 0.004 0.054 523 Dihedral : 3.495 10.572 431 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.88 % Allowed : 23.10 % Favored : 76.02 % 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: 1.62 (0.31), residues: 321 sheet: -0.86 (1.15), residues: 18 loop : -1.33 (0.72), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.001 PHE A 457 TYR 0.021 0.002 TYR A 97 ARG 0.004 0.000 ARG A 447 *********************** 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 67 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.360 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 0.1491 time to fit residues: 12.1215 Evaluate side-chains 61 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0353 time to fit residues: 0.6280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.0170 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- 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: 0.7644 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3171 Z= 0.178 Angle : 0.583 10.383 4304 Z= 0.285 Chirality : 0.038 0.159 549 Planarity : 0.004 0.054 523 Dihedral : 3.555 12.064 431 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.17 % Allowed : 23.68 % Favored : 75.15 % 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: 1.61 (0.31), residues: 317 sheet: -0.89 (1.14), residues: 18 loop : -1.29 (0.70), residues: 69 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 0.025 0.001 PHE A 341 TYR 0.023 0.002 TYR A 97 ARG 0.005 0.000 ARG A 447 ********************** 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 62 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.355 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.1263 time to fit residues: 9.5357 Evaluate side-chains 59 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0321 time to fit residues: 0.5361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.0050 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.189789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.139747 restraints weight = 2186.117| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.35 r_work: 0.3420 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3171 Z= 0.185 Angle : 0.589 10.374 4304 Z= 0.286 Chirality : 0.038 0.161 549 Planarity : 0.004 0.055 523 Dihedral : 3.581 12.573 431 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.29 % Allowed : 24.85 % Favored : 74.85 % 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: 1.44 (0.44), residues: 404 helix: 1.61 (0.31), residues: 315 sheet: -0.88 (1.14), residues: 18 loop : -1.40 (0.71), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.000 0.000 HIS A 41 PHE 0.011 0.001 PHE A 457 TYR 0.023 0.002 TYR A 97 ARG 0.005 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1150.90 seconds wall clock time: 21 minutes 40.37 seconds (1300.37 seconds total)