Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:34:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zs5_11388/11_2022/6zs5_11388.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zs5_11388/11_2022/6zs5_11388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zs5_11388/11_2022/6zs5_11388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zs5_11388/11_2022/6zs5_11388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zs5_11388/11_2022/6zs5_11388.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zs5_11388/11_2022/6zs5_11388.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.082 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2036 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "D" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1036 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 12} Link IDs: {'PTRANS': 6, 'TRANS': 134} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.93, per 1000 atoms: 0.95 Number of scatterers: 2036 At special positions: 0 Unit cell: (72.628, 71.544, 88.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 413 8.00 N 341 7.00 C 1261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 389 " distance=2.04 Simple disulfide: pdb=" SG CYS D 506 " - pdb=" SG CYS D 566 " distance=2.03 Simple disulfide: pdb=" SG CYS D 527 " - pdb=" SG CYS D 582 " distance=1.59 Simple disulfide: pdb=" SG CYS D 571 " - pdb=" SG CYS D 578 " distance=1.89 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 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG B 1 " - " ASN A 396 " " NAG C 1 " - " ASN D 513 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 332.1 milliseconds 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 456 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 43.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 333 removed outlier: 3.661A pdb=" N VAL A 342 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 360 removed outlier: 3.662A pdb=" N ASN A 404 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 419 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 395 removed outlier: 3.662A pdb=" N ASN A 404 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 419 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434 removed outlier: 6.680A pdb=" N TYR D 563 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA D 508 " --> pdb=" O TYR D 563 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS D 565 " --> pdb=" O CYS D 506 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS D 506 " --> pdb=" O HIS D 565 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU D 567 " --> pdb=" O THR D 504 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS D 506 " --> pdb=" O ILE D 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 438 through 440 removed outlier: 6.863A pdb=" N ALA A 438 " --> pdb=" O VAL D 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 458 through 463 removed outlier: 4.017A pdb=" N TYR D 486 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 550 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ARG D 547 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D 538 " --> pdb=" O ARG D 547 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 162 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: 0.49 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 332 1.31 - 1.44: 558 1.44 - 1.57: 1145 1.57 - 1.70: 3 1.70 - 1.83: 31 Bond restraints: 2069 Sorted by residual: bond pdb=" CA SER D 583 " pdb=" C SER D 583 " ideal model delta sigma weight residual 1.520 1.462 0.059 1.20e-02 6.94e+03 2.41e+01 bond pdb=" C SER D 583 " pdb=" O SER D 583 " ideal model delta sigma weight residual 1.234 1.180 0.055 1.15e-02 7.56e+03 2.28e+01 bond pdb=" CA THR D 581 " pdb=" C THR D 581 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.21e-02 6.83e+03 1.06e+01 bond pdb=" CA SER D 583 " pdb=" CB SER D 583 " ideal model delta sigma weight residual 1.533 1.479 0.054 1.69e-02 3.50e+03 1.02e+01 bond pdb=" N THR D 581 " pdb=" CA THR D 581 " ideal model delta sigma weight residual 1.460 1.423 0.036 1.20e-02 6.94e+03 9.24e+00 ... (remaining 2064 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.92: 66 106.92 - 113.71: 1150 113.71 - 120.51: 771 120.51 - 127.31: 795 127.31 - 134.10: 10 Bond angle restraints: 2792 Sorted by residual: angle pdb=" C LYS D 579 " pdb=" N PRO D 580 " pdb=" CA PRO D 580 " ideal model delta sigma weight residual 119.76 125.33 -5.57 1.03e+00 9.43e-01 2.92e+01 angle pdb=" N GLY A 387 " pdb=" CA GLY A 387 " pdb=" C GLY A 387 " ideal model delta sigma weight residual 112.34 123.26 -10.92 2.04e+00 2.40e-01 2.87e+01 angle pdb=" N THR D 581 " pdb=" CA THR D 581 " pdb=" C THR D 581 " ideal model delta sigma weight residual 108.02 100.12 7.90 1.75e+00 3.27e-01 2.04e+01 angle pdb=" C THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta sigma weight residual 110.74 104.22 6.52 1.61e+00 3.86e-01 1.64e+01 angle pdb=" CA PRO D 580 " pdb=" C PRO D 580 " pdb=" N THR D 581 " ideal model delta sigma weight residual 115.56 110.66 4.90 1.27e+00 6.20e-01 1.49e+01 ... (remaining 2787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.56: 1172 22.56 - 45.11: 61 45.11 - 67.66: 8 67.66 - 90.21: 2 90.21 - 112.76: 4 Dihedral angle restraints: 1247 sinusoidal: 526 harmonic: 721 Sorted by residual: dihedral pdb=" CA LYS A 346 " pdb=" C LYS A 346 " pdb=" N CYS A 347 " pdb=" CA CYS A 347 " ideal model delta harmonic sigma weight residual 180.00 150.31 29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" N THR D 581 " pdb=" C THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta harmonic sigma weight residual 123.40 109.35 14.05 0 2.50e+00 1.60e-01 3.16e+01 dihedral pdb=" C THR D 581 " pdb=" N THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta harmonic sigma weight residual -122.00 -108.06 -13.94 0 2.50e+00 1.60e-01 3.11e+01 ... (remaining 1244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 260 0.068 - 0.137: 66 0.137 - 0.205: 4 0.205 - 0.273: 2 0.273 - 0.342: 1 Chirality restraints: 333 Sorted by residual: chirality pdb=" CA THR D 581 " pdb=" N THR D 581 " pdb=" C THR D 581 " pdb=" CB THR D 581 " both_signs ideal model delta sigma weight residual False 2.53 2.87 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB VAL D 487 " pdb=" CA VAL D 487 " pdb=" CG1 VAL D 487 " pdb=" CG2 VAL D 487 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA CYS D 578 " pdb=" N CYS D 578 " pdb=" C CYS D 578 " pdb=" CB CYS D 578 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 330 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 525 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" CG ASP D 525 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP D 525 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP D 525 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 386 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" CG ASP A 386 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 386 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 386 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 387 " -0.041 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A 388 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.035 5.00e-02 4.00e+02 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 186 2.74 - 3.28: 1655 3.28 - 3.82: 2977 3.82 - 4.36: 3207 4.36 - 4.90: 5904 Nonbonded interactions: 13929 Sorted by model distance: nonbonded pdb=" O THR D 581 " pdb=" OG1 THR D 581 " model vdw 2.202 2.440 nonbonded pdb=" OD1 ASP D 532 " pdb=" OG1 THR D 534 " model vdw 2.319 2.440 nonbonded pdb=" OG SER A 362 " pdb=" OD1 ASN A 404 " model vdw 2.342 2.440 nonbonded pdb=" OG SER D 543 " pdb=" N SER D 544 " model vdw 2.348 2.520 nonbonded pdb=" OH TYR A 402 " pdb=" OD2 ASP D 495 " model vdw 2.369 2.440 ... (remaining 13924 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 1261 2.51 5 N 341 2.21 5 O 413 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.000 Extract box with map and model: 6.660 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.020 Process input model: 12.110 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.008 0.067 2069 Z= 0.535 Angle : 1.014 10.920 2792 Z= 0.587 Chirality : 0.062 0.342 333 Planarity : 0.008 0.061 352 Dihedral : 15.423 112.761 776 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.45), residues: 253 helix: None (None), residues: 0 sheet: -1.19 (0.53), residues: 92 loop : -2.61 (0.37), residues: 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.277 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2308 time to fit residues: 16.1946 Evaluate side-chains 44 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 2069 Z= 0.230 Angle : 0.656 7.192 2792 Z= 0.350 Chirality : 0.046 0.172 333 Planarity : 0.005 0.044 352 Dihedral : 12.508 114.559 333 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 4.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.47), residues: 253 helix: None (None), residues: 0 sheet: -0.51 (0.50), residues: 100 loop : -2.32 (0.42), residues: 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.261 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.1469 time to fit residues: 8.8697 Evaluate side-chains 48 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.231 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0241 time to fit residues: 0.5752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.0040 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN D 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 2069 Z= 0.188 Angle : 0.604 6.757 2792 Z= 0.324 Chirality : 0.046 0.198 333 Planarity : 0.004 0.038 352 Dihedral : 12.355 114.173 333 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 4.19 % 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 (0.48), residues: 253 helix: None (None), residues: 0 sheet: -0.07 (0.50), residues: 98 loop : -1.99 (0.44), residues: 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.244 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 51 average time/residue: 0.1520 time to fit residues: 8.9463 Evaluate side-chains 44 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0355 time to fit residues: 0.5574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 2069 Z= 0.195 Angle : 0.597 6.576 2792 Z= 0.316 Chirality : 0.045 0.134 333 Planarity : 0.004 0.037 352 Dihedral : 12.315 114.333 333 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 6.51 % 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 (0.49), residues: 253 helix: None (None), residues: 0 sheet: -0.08 (0.50), residues: 98 loop : -1.84 (0.45), residues: 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.246 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 48 average time/residue: 0.1602 time to fit residues: 8.8379 Evaluate side-chains 49 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.249 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0471 time to fit residues: 1.0196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 2069 Z= 0.247 Angle : 0.623 5.993 2792 Z= 0.327 Chirality : 0.046 0.139 333 Planarity : 0.004 0.041 352 Dihedral : 12.393 114.273 333 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.86 % 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: -1.69 (0.48), residues: 253 helix: None (None), residues: 0 sheet: 0.09 (0.51), residues: 90 loop : -1.96 (0.44), residues: 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.272 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 46 average time/residue: 0.1785 time to fit residues: 9.5041 Evaluate side-chains 39 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0485 time to fit residues: 0.4163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.7944 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 2069 Z= 0.174 Angle : 0.632 8.857 2792 Z= 0.315 Chirality : 0.045 0.139 333 Planarity : 0.003 0.039 352 Dihedral : 12.355 114.154 333 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.49), residues: 253 helix: -3.96 (1.18), residues: 6 sheet: 0.32 (0.52), residues: 89 loop : -1.94 (0.45), residues: 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.243 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.1692 time to fit residues: 9.4596 Evaluate side-chains 42 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.251 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0242 time to fit residues: 0.4933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.7985 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 2069 Z= 0.246 Angle : 0.672 8.569 2792 Z= 0.338 Chirality : 0.045 0.134 333 Planarity : 0.004 0.040 352 Dihedral : 12.373 114.250 333 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 3.26 % 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: -1.51 (0.50), residues: 253 helix: None (None), residues: 0 sheet: 0.27 (0.52), residues: 90 loop : -1.87 (0.46), residues: 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.258 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.1759 time to fit residues: 8.8620 Evaluate side-chains 44 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0838 time to fit residues: 0.8296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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: 0.7970 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 2069 Z= 0.202 Angle : 0.648 8.062 2792 Z= 0.325 Chirality : 0.045 0.130 333 Planarity : 0.004 0.041 352 Dihedral : 12.387 114.071 333 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.86 % 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: -1.47 (0.50), residues: 253 helix: None (None), residues: 0 sheet: 0.30 (0.52), residues: 90 loop : -1.85 (0.46), residues: 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.263 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.1765 time to fit residues: 8.4902 Evaluate side-chains 43 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0280 time to fit residues: 0.4309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 2069 Z= 0.220 Angle : 0.650 7.703 2792 Z= 0.326 Chirality : 0.045 0.128 333 Planarity : 0.003 0.041 352 Dihedral : 12.377 114.125 333 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.40 % 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 (0.50), residues: 253 helix: None (None), residues: 0 sheet: 0.22 (0.52), residues: 90 loop : -1.88 (0.46), residues: 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.248 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 0.1758 time to fit residues: 8.6407 Evaluate side-chains 43 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0311 time to fit residues: 0.4714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.0870 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- 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: 0.8005 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 2069 Z= 0.245 Angle : 0.664 7.520 2792 Z= 0.335 Chirality : 0.045 0.140 333 Planarity : 0.004 0.043 352 Dihedral : 12.428 113.861 333 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.00 % 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: -1.57 (0.50), residues: 253 helix: None (None), residues: 0 sheet: 0.17 (0.53), residues: 90 loop : -1.88 (0.46), residues: 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.256 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1691 time to fit residues: 8.1392 Evaluate side-chains 40 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.222 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.0970 chunk 20 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 0.0570 overall best weight: 0.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 575 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.088972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.075782 restraints weight = 5924.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.077789 restraints weight = 3115.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.079120 restraints weight = 2032.470| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 2069 Z= 0.180 Angle : 0.651 7.539 2792 Z= 0.322 Chirality : 0.044 0.141 333 Planarity : 0.003 0.037 352 Dihedral : 12.348 114.112 333 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.50), residues: 253 helix: -4.49 (0.61), residues: 6 sheet: 0.34 (0.54), residues: 89 loop : -1.96 (0.46), residues: 158 =============================================================================== Job complete usr+sys time: 1024.18 seconds wall clock time: 18 minutes 52.97 seconds (1132.97 seconds total)