Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 18:17:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/10_2023/8jjo_36361_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/10_2023/8jjo_36361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/10_2023/8jjo_36361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/10_2023/8jjo_36361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/10_2023/8jjo_36361_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/10_2023/8jjo_36361_neut_updated.pdb" } resolution = 3.4 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= -0.002 sd= 0.158 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 1980 2.51 5 N 487 2.21 5 O 529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 122": "OE1" <-> "OE2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 238": "OE1" <-> "OE2" Residue "F ASP 242": "OD1" <-> "OD2" Residue "F ASP 296": "OD1" <-> "OD2" Residue "F TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 335": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 3016 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2998 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 8, 'TRANS': 366} Chain breaks: 1 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'JTZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.05, per 1000 atoms: 0.68 Number of scatterers: 3016 At special positions: 0 Unit cell: (54.57, 81.32, 107, 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 20 16.00 O 529 8.00 N 487 7.00 C 1980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 106 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 190 " distance=2.03 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: 1.21 Conformation dependent library (CDL) restraints added in 390.6 milliseconds 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 722 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 0 sheets defined 74.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'F' and resid 30 through 60 removed outlier: 3.703A pdb=" N VAL F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY F 37 " --> pdb=" O VAL F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 85 Processing helix chain 'F' and resid 87 through 95 Processing helix chain 'F' and resid 107 through 133 Processing helix chain 'F' and resid 147 through 169 removed outlier: 4.093A pdb=" N LEU F 167 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Proline residue: F 168 - end of helix Processing helix chain 'F' and resid 179 through 182 No H-bonds generated for 'chain 'F' and resid 179 through 182' Processing helix chain 'F' and resid 197 through 206 Processing helix chain 'F' and resid 211 through 236 removed outlier: 3.560A pdb=" N VAL F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS F 227 " --> pdb=" O PHE F 223 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG F 228 " --> pdb=" O GLN F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'F' and resid 253 through 272 Processing helix chain 'F' and resid 280 through 299 Processing helix chain 'F' and resid 310 through 365 removed outlier: 4.393A pdb=" N GLN F 326 " --> pdb=" O ASN F 322 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS F 340 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR F 350 " --> pdb=" O MET F 346 " (cutoff:3.500A) Proline residue: F 355 - end of helix removed outlier: 3.506A pdb=" N VAL F 359 " --> pdb=" O PRO F 355 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE F 361 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL F 362 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL F 364 " --> pdb=" O ASN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 395 removed outlier: 3.909A pdb=" N GLY F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER F 386 " --> pdb=" O GLY F 382 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY F 387 " --> pdb=" O TYR F 383 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE F 388 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN F 389 " --> pdb=" O ASN F 385 " (cutoff:3.500A) Proline residue: F 390 - end of helix removed outlier: 3.714A pdb=" N ARG F 395 " --> pdb=" O LEU F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 404 removed outlier: 3.525A pdb=" N ALA F 402 " --> pdb=" O ASP F 398 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 588 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: 0.75 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 930 1.34 - 1.46: 738 1.46 - 1.58: 1384 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 3083 Sorted by residual: bond pdb=" C12 JTZ F 501 " pdb=" C7 JTZ F 501 " ideal model delta sigma weight residual 1.403 1.353 0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C2 JTZ F 501 " pdb=" N1 JTZ F 501 " ideal model delta sigma weight residual 1.458 1.417 0.041 2.00e-02 2.50e+03 4.14e+00 bond pdb=" C8 JTZ F 501 " pdb=" C9 JTZ F 501 " ideal model delta sigma weight residual 1.390 1.352 0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" C7 JTZ F 501 " pdb=" C8 JTZ F 501 " ideal model delta sigma weight residual 1.393 1.357 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" C10 JTZ F 501 " pdb=" C9 JTZ F 501 " ideal model delta sigma weight residual 1.385 1.351 0.034 2.00e-02 2.50e+03 2.88e+00 ... (remaining 3078 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.16: 52 106.16 - 113.11: 1689 113.11 - 120.06: 1100 120.06 - 127.01: 1311 127.01 - 133.95: 32 Bond angle restraints: 4184 Sorted by residual: angle pdb=" C1 JTZ F 501 " pdb=" C2 JTZ F 501 " pdb=" N1 JTZ F 501 " ideal model delta sigma weight residual 114.33 105.42 8.91 3.00e+00 1.11e-01 8.83e+00 angle pdb=" C2 JTZ F 501 " pdb=" N1 JTZ F 501 " pdb=" C4 JTZ F 501 " ideal model delta sigma weight residual 115.12 106.67 8.45 3.00e+00 1.11e-01 7.93e+00 angle pdb=" N TRP F 105 " pdb=" CA TRP F 105 " pdb=" C TRP F 105 " ideal model delta sigma weight residual 113.38 110.14 3.24 1.17e+00 7.31e-01 7.69e+00 angle pdb=" C ASP F 367 " pdb=" N ASN F 368 " pdb=" CA ASN F 368 " ideal model delta sigma weight residual 121.54 126.63 -5.09 1.91e+00 2.74e-01 7.09e+00 angle pdb=" C6 JTZ F 501 " pdb=" C5 JTZ F 501 " pdb=" O1 JTZ F 501 " ideal model delta sigma weight residual 112.06 104.46 7.60 3.00e+00 1.11e-01 6.42e+00 ... (remaining 4179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1553 17.96 - 35.92: 203 35.92 - 53.89: 50 53.89 - 71.85: 4 71.85 - 89.81: 7 Dihedral angle restraints: 1817 sinusoidal: 709 harmonic: 1108 Sorted by residual: dihedral pdb=" CB CYS F 184 " pdb=" SG CYS F 184 " pdb=" SG CYS F 190 " pdb=" CB CYS F 190 " ideal model delta sinusoidal sigma weight residual -86.00 0.68 -86.68 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS F 106 " pdb=" SG CYS F 106 " pdb=" SG CYS F 191 " pdb=" CB CYS F 191 " ideal model delta sinusoidal sigma weight residual -86.00 -162.86 76.86 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CA ASP F 251 " pdb=" C ASP F 251 " pdb=" N ASN F 252 " pdb=" CA ASN F 252 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 1814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 430 0.060 - 0.120: 56 0.120 - 0.181: 1 0.181 - 0.241: 0 0.241 - 0.301: 1 Chirality restraints: 488 Sorted by residual: chirality pdb=" C5 JTZ F 501 " pdb=" C4 JTZ F 501 " pdb=" C6 JTZ F 501 " pdb=" O1 JTZ F 501 " both_signs ideal model delta sigma weight residual False -2.33 -2.63 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE F 370 " pdb=" CA ILE F 370 " pdb=" CG1 ILE F 370 " pdb=" CG2 ILE F 370 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ASN F 368 " pdb=" N ASN F 368 " pdb=" C ASN F 368 " pdb=" CB ASN F 368 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 485 not shown) Planarity restraints: 513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 237 " 0.003 2.00e-02 2.50e+03 8.53e-03 1.82e+00 pdb=" CG TRP F 237 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP F 237 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP F 237 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 237 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP F 237 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 237 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 237 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 237 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 237 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 385 " 0.006 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" C ASN F 385 " -0.019 2.00e-02 2.50e+03 pdb=" O ASN F 385 " 0.007 2.00e-02 2.50e+03 pdb=" N SER F 386 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 354 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO F 355 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO F 355 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 355 " -0.015 5.00e-02 4.00e+02 ... (remaining 510 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 142 2.73 - 3.27: 3232 3.27 - 3.81: 5053 3.81 - 4.36: 5656 4.36 - 4.90: 9751 Nonbonded interactions: 23834 Sorted by model distance: nonbonded pdb=" OH TYR F 219 " pdb=" O LEU F 339 " model vdw 2.184 2.440 nonbonded pdb=" OD2 ASP F 113 " pdb=" OH TYR F 383 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR F 118 " pdb=" OG SER F 207 " model vdw 2.276 2.440 nonbonded pdb=" O ALA F 119 " pdb=" OG1 THR F 123 " model vdw 2.377 2.440 nonbonded pdb=" C4 JTZ F 501 " pdb=" O2 JTZ F 501 " model vdw 2.378 2.752 ... (remaining 23829 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.370 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.950 Find NCS groups from input model: 0.080 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 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 0.050 3083 Z= 0.230 Angle : 0.637 8.912 4184 Z= 0.328 Chirality : 0.041 0.301 488 Planarity : 0.003 0.027 513 Dihedral : 17.030 89.810 1089 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.31 % Allowed : 17.96 % Favored : 81.73 % 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: -0.11 (0.44), residues: 371 helix: 0.85 (0.31), residues: 293 sheet: None (None), residues: 0 loop : -3.64 (0.54), residues: 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.341 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.1156 time to fit residues: 8.0661 Evaluate side-chains 54 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0451 time to fit residues: 0.5428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN F 360 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3083 Z= 0.177 Angle : 0.501 5.612 4184 Z= 0.266 Chirality : 0.038 0.110 488 Planarity : 0.003 0.026 513 Dihedral : 5.464 53.214 403 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.79 % Allowed : 18.58 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.45), residues: 371 helix: 1.19 (0.31), residues: 298 sheet: None (None), residues: 0 loop : -3.96 (0.52), residues: 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.329 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 0.1062 time to fit residues: 8.8219 Evaluate side-chains 58 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0350 time to fit residues: 0.7331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3083 Z= 0.192 Angle : 0.488 5.626 4184 Z= 0.260 Chirality : 0.038 0.108 488 Planarity : 0.003 0.027 513 Dihedral : 5.252 46.465 403 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.79 % Allowed : 20.74 % Favored : 76.47 % 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: 0.48 (0.45), residues: 371 helix: 1.27 (0.31), residues: 299 sheet: None (None), residues: 0 loop : -3.85 (0.54), residues: 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.340 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 65 average time/residue: 0.1077 time to fit residues: 9.1030 Evaluate side-chains 58 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.306 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0357 time to fit residues: 0.7426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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: 0.6880 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3083 Z= 0.209 Angle : 0.516 9.438 4184 Z= 0.268 Chirality : 0.038 0.111 488 Planarity : 0.003 0.027 513 Dihedral : 5.142 38.350 403 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.48 % Allowed : 23.53 % Favored : 73.99 % 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: 0.46 (0.45), residues: 371 helix: 1.29 (0.31), residues: 297 sheet: None (None), residues: 0 loop : -3.90 (0.52), residues: 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.303 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.0956 time to fit residues: 8.2962 Evaluate side-chains 60 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0365 time to fit residues: 0.7995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.0010 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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: 0.6836 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3083 Z= 0.172 Angle : 0.506 8.344 4184 Z= 0.262 Chirality : 0.037 0.106 488 Planarity : 0.003 0.029 513 Dihedral : 4.918 29.771 403 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.93 % Allowed : 24.46 % Favored : 74.61 % 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: 0.67 (0.46), residues: 371 helix: 1.37 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -3.96 (0.54), residues: 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.303 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 60 average time/residue: 0.0968 time to fit residues: 7.7779 Evaluate side-chains 58 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0351 time to fit residues: 0.5689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.6848 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3083 Z= 0.186 Angle : 0.514 9.097 4184 Z= 0.265 Chirality : 0.037 0.108 488 Planarity : 0.003 0.029 513 Dihedral : 4.778 21.345 403 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.24 % Allowed : 25.70 % Favored : 73.07 % 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: 0.62 (0.45), residues: 371 helix: 1.32 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.97 (0.51), residues: 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.348 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.1015 time to fit residues: 8.2277 Evaluate side-chains 58 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0329 time to fit residues: 0.6452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3083 Z= 0.183 Angle : 0.517 9.166 4184 Z= 0.265 Chirality : 0.037 0.109 488 Planarity : 0.003 0.029 513 Dihedral : 4.744 21.685 403 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.55 % Allowed : 24.15 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.45), residues: 371 helix: 1.31 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.98 (0.51), residues: 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.316 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.0985 time to fit residues: 7.5233 Evaluate side-chains 58 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0369 time to fit residues: 0.6500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 ASN F 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3083 Z= 0.176 Angle : 0.514 9.033 4184 Z= 0.266 Chirality : 0.037 0.107 488 Planarity : 0.003 0.029 513 Dihedral : 4.764 23.860 403 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.66 % Favored : 93.80 % Rotamer: Outliers : 0.93 % Allowed : 24.46 % Favored : 74.61 % 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: 0.68 (0.46), residues: 371 helix: 1.36 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.91 (0.52), residues: 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.310 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 0.1025 time to fit residues: 8.5288 Evaluate side-chains 58 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0344 time to fit residues: 0.6148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.0570 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3083 Z= 0.155 Angle : 0.504 9.057 4184 Z= 0.258 Chirality : 0.036 0.104 488 Planarity : 0.003 0.029 513 Dihedral : 4.738 27.990 403 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.66 % Favored : 94.07 % Rotamer: Outliers : 0.62 % Allowed : 25.39 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.46), residues: 371 helix: 1.46 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.93 (0.51), residues: 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.322 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.0996 time to fit residues: 7.8471 Evaluate side-chains 58 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0406 time to fit residues: 0.5175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3083 Z= 0.178 Angle : 0.527 8.974 4184 Z= 0.271 Chirality : 0.037 0.108 488 Planarity : 0.003 0.029 513 Dihedral : 4.825 30.032 403 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.12 % Favored : 94.34 % Rotamer: Outliers : 0.93 % Allowed : 25.70 % Favored : 73.37 % 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: 0.90 (0.46), residues: 371 helix: 1.55 (0.32), residues: 298 sheet: None (None), residues: 0 loop : -3.59 (0.50), residues: 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.331 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 0.1018 time to fit residues: 7.9731 Evaluate side-chains 61 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0503 time to fit residues: 0.6266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.0670 chunk 5 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.219355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.173311 restraints weight = 3412.706| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.43 r_work: 0.4043 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3083 Z= 0.155 Angle : 0.511 9.011 4184 Z= 0.265 Chirality : 0.037 0.106 488 Planarity : 0.003 0.029 513 Dihedral : 4.867 33.600 403 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.12 % Favored : 94.61 % Rotamer: Outliers : 0.62 % Allowed : 26.01 % Favored : 73.37 % 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: 0.96 (0.46), residues: 371 helix: 1.59 (0.32), residues: 298 sheet: None (None), residues: 0 loop : -3.55 (0.51), residues: 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1030.02 seconds wall clock time: 19 minutes 7.10 seconds (1147.10 seconds total)