Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:38:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/11_2022/6ski_10225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/11_2022/6ski_10225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/11_2022/6ski_10225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/11_2022/6ski_10225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/11_2022/6ski_10225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/11_2022/6ski_10225.pdb" } resolution = 2.6 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= -0.000 sd= 1.000 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: 4434 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4092 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 498} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 342 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 2.90, per 1000 atoms: 0.65 Number of scatterers: 4434 At special positions: 0 Unit cell: (65.536, 71.68, 124.928, 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 19 16.00 O 821 8.00 N 776 7.00 C 2818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 663.5 milliseconds 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1038 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 8 sheets defined 32.5% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'F' and resid 52 through 59 Processing helix chain 'F' and resid 71 through 86 Processing helix chain 'F' and resid 100 through 109 Processing helix chain 'F' and resid 144 through 155 removed outlier: 4.149A pdb=" N THR F 148 " --> pdb=" O MET F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 179 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.580A pdb=" N ALA F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 348 Processing helix chain 'F' and resid 349 through 363 Processing helix chain 'F' and resid 371 through 375 Processing helix chain 'F' and resid 388 through 395 Processing helix chain 'F' and resid 415 through 432 removed outlier: 3.771A pdb=" N VAL F 419 " --> pdb=" O ASP F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 451 through 467 Processing helix chain 'F' and resid 475 through 484 Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.726A pdb=" N ILE F 533 " --> pdb=" O ASP F 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 4 through 9 removed outlier: 4.316A pdb=" N TYR F 4 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE F 184 " --> pdb=" O PRO F 31 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG F 33 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE F 186 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL F 35 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 188 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 12.031A pdb=" N VAL F 238 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 10.206A pdb=" N ILE F 189 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N PHE F 240 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE F 191 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY F 242 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL F 193 " --> pdb=" O GLY F 242 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N LYS F 278 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG F 239 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE F 280 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU F 241 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE F 282 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU F 243 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ALA F 284 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU F 304 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN F 281 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU F 306 " --> pdb=" O GLN F 281 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR F 283 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 121 through 128 Processing sheet with id=AA3, first strand: chain 'F' and resid 294 through 296 removed outlier: 6.612A pdb=" N LEU F 294 " --> pdb=" O TRP F 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 328 through 331 Processing sheet with id=AA5, first strand: chain 'F' and resid 328 through 331 removed outlier: 4.568A pdb=" N GLN F 398 " --> pdb=" O VAL F 386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 495 through 497 Processing sheet with id=AA7, first strand: chain 'F' and resid 500 through 502 Processing sheet with id=AA8, first strand: chain 'A' and resid 806 through 809 184 hydrogen bonds defined for protein. 516 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: 1.18 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1472 1.34 - 1.46: 874 1.46 - 1.57: 2150 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4528 Sorted by residual: bond pdb=" C LYS F 29 " pdb=" N LYS F 30 " ideal model delta sigma weight residual 1.331 1.290 0.041 2.07e-02 2.33e+03 4.01e+00 bond pdb=" CA ARG F 198 " pdb=" C ARG F 198 " ideal model delta sigma weight residual 1.521 1.499 0.021 1.27e-02 6.20e+03 2.86e+00 bond pdb=" N GLY F 199 " pdb=" CA GLY F 199 " ideal model delta sigma weight residual 1.447 1.423 0.024 1.58e-02 4.01e+03 2.35e+00 bond pdb=" CA ASP F 245 " pdb=" C ASP F 245 " ideal model delta sigma weight residual 1.533 1.519 0.014 9.60e-03 1.09e+04 2.08e+00 bond pdb=" C SER F 197 " pdb=" N ARG F 198 " ideal model delta sigma weight residual 1.335 1.316 0.019 1.42e-02 4.96e+03 1.72e+00 ... (remaining 4523 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.24: 165 107.24 - 113.93: 2516 113.93 - 120.63: 1791 120.63 - 127.32: 1595 127.32 - 134.01: 52 Bond angle restraints: 6119 Sorted by residual: angle pdb=" C PHE F 196 " pdb=" N SER F 197 " pdb=" CA SER F 197 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.12e+01 angle pdb=" N ARG F 198 " pdb=" CA ARG F 198 " pdb=" C ARG F 198 " ideal model delta sigma weight residual 113.97 109.37 4.60 1.28e+00 6.10e-01 1.29e+01 angle pdb=" N SER F 197 " pdb=" CA SER F 197 " pdb=" C SER F 197 " ideal model delta sigma weight residual 110.80 117.52 -6.72 2.13e+00 2.20e-01 9.95e+00 angle pdb=" C GLY F 199 " pdb=" N ALA F 200 " pdb=" CA ALA F 200 " ideal model delta sigma weight residual 121.80 115.35 6.45 2.16e+00 2.14e-01 8.93e+00 angle pdb=" C SER F 197 " pdb=" N ARG F 198 " pdb=" CA ARG F 198 " ideal model delta sigma weight residual 122.11 117.72 4.39 1.64e+00 3.72e-01 7.16e+00 ... (remaining 6114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 2317 16.88 - 33.75: 278 33.75 - 50.63: 83 50.63 - 67.51: 17 67.51 - 84.38: 2 Dihedral angle restraints: 2697 sinusoidal: 1080 harmonic: 1617 Sorted by residual: dihedral pdb=" CA ARG F 198 " pdb=" C ARG F 198 " pdb=" N GLY F 199 " pdb=" CA GLY F 199 " ideal model delta harmonic sigma weight residual 180.00 147.70 32.30 0 5.00e+00 4.00e-02 4.17e+01 dihedral pdb=" CA LEU F 294 " pdb=" C LEU F 294 " pdb=" N ASN F 295 " pdb=" CA ASN F 295 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA SER F 329 " pdb=" C SER F 329 " pdb=" N LEU F 330 " pdb=" CA LEU F 330 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 2694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 393 0.033 - 0.066: 194 0.066 - 0.099: 53 0.099 - 0.132: 24 0.132 - 0.165: 1 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA PRO A 792 " pdb=" N PRO A 792 " pdb=" C PRO A 792 " pdb=" CB PRO A 792 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE A 809 " pdb=" N ILE A 809 " pdb=" C ILE A 809 " pdb=" CB ILE A 809 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA PRO F 273 " pdb=" N PRO F 273 " pdb=" C PRO F 273 " pdb=" CB PRO F 273 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 662 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 197 " -0.028 2.00e-02 2.50e+03 5.55e-02 3.08e+01 pdb=" C SER F 197 " 0.096 2.00e-02 2.50e+03 pdb=" O SER F 197 " -0.035 2.00e-02 2.50e+03 pdb=" N ARG F 198 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 204 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C ARG F 204 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG F 204 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS F 205 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 200 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ALA F 200 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA F 200 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA F 201 " 0.010 2.00e-02 2.50e+03 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 577 2.75 - 3.29: 4159 3.29 - 3.82: 7966 3.82 - 4.36: 9931 4.36 - 4.90: 16178 Nonbonded interactions: 38811 Sorted by model distance: nonbonded pdb=" NH2 ARG F 422 " pdb=" O LEU F 445 " model vdw 2.210 2.520 nonbonded pdb=" OD2 ASP F 44 " pdb=" OH TYR F 127 " model vdw 2.270 2.440 nonbonded pdb=" O SER F 181 " pdb=" OG SER F 181 " model vdw 2.285 2.440 nonbonded pdb=" O SER F 274 " pdb=" OG SER F 274 " model vdw 2.295 2.440 nonbonded pdb=" OD2 ASP F 192 " pdb=" NH2 ARG F 239 " model vdw 2.303 2.520 ... (remaining 38806 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 19 5.16 5 C 2818 2.51 5 N 776 2.21 5 O 821 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 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: 1.500 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: 9.390 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 15.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.004 0.041 4528 Z= 0.291 Angle : 0.723 10.660 6119 Z= 0.408 Chirality : 0.043 0.165 665 Planarity : 0.005 0.056 800 Dihedral : 16.205 84.384 1659 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.80 (0.33), residues: 557 helix: -0.58 (0.35), residues: 169 sheet: 0.20 (0.44), residues: 116 loop : -0.72 (0.38), residues: 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.558 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 1.1631 time to fit residues: 112.2258 Evaluate side-chains 69 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.7443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 106 ASN F 110 HIS F 123 GLN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN F 281 GLN F 286 ASN F 295 ASN F 387 ASN F 487 HIS F 493 ASN F 512 HIS A 791 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 4528 Z= 0.243 Angle : 0.601 9.247 6119 Z= 0.316 Chirality : 0.043 0.159 665 Planarity : 0.004 0.050 800 Dihedral : 5.234 30.190 609 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.09 (0.35), residues: 557 helix: 0.76 (0.39), residues: 165 sheet: 0.30 (0.46), residues: 114 loop : -0.39 (0.39), residues: 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.559 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 82 average time/residue: 1.1930 time to fit residues: 101.5606 Evaluate side-chains 73 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.5930 time to fit residues: 1.9984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 GLN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4528 Z= 0.200 Angle : 0.550 8.745 6119 Z= 0.289 Chirality : 0.042 0.145 665 Planarity : 0.004 0.049 800 Dihedral : 4.986 32.667 609 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.44 (0.35), residues: 557 helix: 1.12 (0.39), residues: 166 sheet: 0.67 (0.50), residues: 93 loop : -0.25 (0.37), residues: 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.559 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 1.1324 time to fit residues: 89.7099 Evaluate side-chains 69 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0469 time to fit residues: 0.8965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN A 791 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 4528 Z= 0.276 Angle : 0.564 8.825 6119 Z= 0.299 Chirality : 0.043 0.148 665 Planarity : 0.004 0.050 800 Dihedral : 5.083 34.094 609 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.44 (0.35), residues: 557 helix: 1.20 (0.39), residues: 166 sheet: 0.14 (0.46), residues: 113 loop : -0.10 (0.39), residues: 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.564 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 1.1097 time to fit residues: 83.3563 Evaluate side-chains 68 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0524 time to fit residues: 0.8494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 GLN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 4528 Z= 0.308 Angle : 0.574 8.879 6119 Z= 0.306 Chirality : 0.043 0.150 665 Planarity : 0.004 0.050 800 Dihedral : 5.136 34.265 609 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.47 (0.35), residues: 557 helix: 1.21 (0.38), residues: 166 sheet: 0.03 (0.46), residues: 113 loop : -0.00 (0.39), residues: 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.535 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 71 average time/residue: 1.0701 time to fit residues: 79.3556 Evaluate side-chains 72 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.562 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.3826 time to fit residues: 1.9952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4528 Z= 0.177 Angle : 0.520 8.692 6119 Z= 0.275 Chirality : 0.042 0.140 665 Planarity : 0.004 0.047 800 Dihedral : 4.806 34.975 609 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.65 (0.35), residues: 557 helix: 1.51 (0.39), residues: 166 sheet: 0.02 (0.45), residues: 111 loop : 0.05 (0.39), residues: 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.545 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 75 average time/residue: 1.1350 time to fit residues: 88.8626 Evaluate side-chains 66 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.7646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.0470 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4528 Z= 0.171 Angle : 0.522 8.591 6119 Z= 0.274 Chirality : 0.042 0.135 665 Planarity : 0.004 0.047 800 Dihedral : 4.701 35.277 609 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.75 (0.35), residues: 557 helix: 1.69 (0.39), residues: 166 sheet: 0.07 (0.46), residues: 111 loop : 0.04 (0.38), residues: 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.575 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 1.1277 time to fit residues: 83.5236 Evaluate side-chains 70 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.0681 time to fit residues: 1.7755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN A 791 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4528 Z= 0.218 Angle : 0.527 8.648 6119 Z= 0.281 Chirality : 0.042 0.136 665 Planarity : 0.004 0.048 800 Dihedral : 4.805 35.393 609 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.75 (0.35), residues: 557 helix: 1.66 (0.39), residues: 166 sheet: 0.07 (0.47), residues: 111 loop : 0.07 (0.39), residues: 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.541 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 1.1742 time to fit residues: 84.4150 Evaluate side-chains 68 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.544 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.1337 time to fit residues: 1.9048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.0470 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.0170 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4528 Z= 0.195 Angle : 0.522 8.624 6119 Z= 0.276 Chirality : 0.042 0.134 665 Planarity : 0.004 0.048 800 Dihedral : 4.742 35.258 609 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.78 (0.35), residues: 557 helix: 1.75 (0.39), residues: 166 sheet: 0.05 (0.47), residues: 111 loop : 0.06 (0.38), residues: 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.588 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 67 average time/residue: 1.0429 time to fit residues: 73.0846 Evaluate side-chains 68 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0445 time to fit residues: 0.8096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4528 Z= 0.224 Angle : 0.526 8.662 6119 Z= 0.278 Chirality : 0.042 0.138 665 Planarity : 0.004 0.048 800 Dihedral : 4.815 35.361 609 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.76 (0.35), residues: 557 helix: 1.72 (0.39), residues: 166 sheet: 0.04 (0.47), residues: 111 loop : 0.05 (0.38), residues: 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.545 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 67 average time/residue: 1.0609 time to fit residues: 74.3345 Evaluate side-chains 66 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.7171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099779 restraints weight = 5351.426| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.68 r_work: 0.3238 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 1.49 restraints_weight: 0.2500 r_work: 0.3218 rms_B_bonded: 1.53 restraints_weight: 0.1250 r_work: 0.3207 rms_B_bonded: 1.61 restraints_weight: 0.0625 r_work: 0.3195 rms_B_bonded: 1.72 restraints_weight: 0.0312 r_work: 0.3183 rms_B_bonded: 1.86 restraints_weight: 0.0156 r_work: 0.3170 rms_B_bonded: 2.04 restraints_weight: 0.0078 r_work: 0.3155 rms_B_bonded: 2.24 restraints_weight: 0.0039 r_work: 0.3139 rms_B_bonded: 2.49 restraints_weight: 0.0020 r_work: 0.3122 rms_B_bonded: 2.77 restraints_weight: 0.0010 r_work: 0.3104 rms_B_bonded: 3.10 restraints_weight: 0.0005 r_work: 0.3083 rms_B_bonded: 3.48 restraints_weight: 0.0002 r_work: 0.3061 rms_B_bonded: 3.91 restraints_weight: 0.0001 r_work: 0.3036 rms_B_bonded: 4.41 restraints_weight: 0.0001 r_work: 0.3009 rms_B_bonded: 4.98 restraints_weight: 0.0000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4528 Z= 0.205 Angle : 0.538 8.667 6119 Z= 0.280 Chirality : 0.042 0.137 665 Planarity : 0.004 0.048 800 Dihedral : 4.768 35.274 609 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.77 (0.35), residues: 557 helix: 1.76 (0.39), residues: 166 sheet: 0.03 (0.47), residues: 111 loop : 0.04 (0.38), residues: 280 =============================================================================== Job complete usr+sys time: 2023.89 seconds wall clock time: 36 minutes 42.61 seconds (2202.61 seconds total)