Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:00:10 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/12_2021/6ski_10225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/12_2021/6ski_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_10225/12_2021/6ski_10225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/12_2021/6ski_10225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/12_2021/6ski_10225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/12_2021/6ski_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 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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: 2.83, per 1000 atoms: 0.64 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 Amimo 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: 1.91 Conformation dependent library (CDL) restraints added in 686.5 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: 0.26 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: 1.51 Time building geometry restraints manager: 2.05 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 Write .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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.070 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 17.290 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:12.720 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 41.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.538 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 1.2123 time to fit residues: 117.0532 Evaluate side-chains 69 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.7336 ------------------------------------------------------------------------------- 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 14 HIS 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1513 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= 0.244 Angle : 0.600 9.189 6119 Z= 0.315 Chirality : 0.043 0.159 665 Planarity : 0.005 0.050 800 Dihedral : 5.226 30.222 609 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.82 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: 0.13 (0.35), residues: 557 helix: 0.77 (0.39), residues: 165 sheet: 0.74 (0.51), residues: 93 loop : -0.47 (0.37), residues: 299 *********************** 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 87 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.571 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 82 average time/residue: 1.1721 time to fit residues: 99.9954 Evaluate side-chains 72 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.1330 time to fit residues: 1.9149 ------------------------------------------------------------------------------- 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: 0.2980 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8286 moved from start: 0.1863 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= 0.213 Angle : 0.553 8.773 6119 Z= 0.292 Chirality : 0.042 0.144 665 Planarity : 0.004 0.049 800 Dihedral : 5.010 32.799 609 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 0.44 (0.35), residues: 557 helix: 1.13 (0.39), residues: 166 sheet: 0.66 (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 78 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.528 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 75 average time/residue: 1.0927 time to fit residues: 85.8049 Evaluate side-chains 70 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0479 time to fit residues: 0.8851 ------------------------------------------------------------------------------- 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: 0.6980 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 A 791 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1971 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= 0.325 Angle : 0.582 8.875 6119 Z= 0.310 Chirality : 0.043 0.150 665 Planarity : 0.004 0.051 800 Dihedral : 5.186 34.256 609 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: 0.35 (0.35), residues: 557 helix: 1.10 (0.38), residues: 166 sheet: 0.04 (0.45), residues: 113 loop : -0.11 (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 77 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.506 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 72 average time/residue: 0.9884 time to fit residues: 74.5729 Evaluate side-chains 66 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0432 time to fit residues: 0.8072 ------------------------------------------------------------------------------- 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: 0.5980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.0050 chunk 31 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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: 0.8268 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 4528 Z= 0.172 Angle : 0.514 8.657 6119 Z= 0.272 Chirality : 0.042 0.137 665 Planarity : 0.004 0.047 800 Dihedral : 4.777 34.622 609 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 1.08 % 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: 0.54 (0.35), residues: 557 helix: 1.46 (0.39), residues: 166 sheet: 0.07 (0.46), residues: 113 loop : -0.09 (0.38), 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 66 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.583 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 66 average time/residue: 1.0592 time to fit residues: 73.2283 Evaluate side-chains 63 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.7306 ------------------------------------------------------------------------------- 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: 0.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8287 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4528 Z= 0.211 Angle : 0.528 8.595 6119 Z= 0.279 Chirality : 0.042 0.138 665 Planarity : 0.004 0.048 800 Dihedral : 4.837 35.449 609 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.39 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: 0.65 (0.35), residues: 557 helix: 1.53 (0.39), residues: 166 sheet: 0.05 (0.46), residues: 111 loop : 0.03 (0.38), 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 70 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.563 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 69 average time/residue: 1.1831 time to fit residues: 85.1261 Evaluate side-chains 64 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.3915 time to fit residues: 2.1809 ------------------------------------------------------------------------------- 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: 0.5980 chunk 45 optimal weight: 0.0060 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.0060 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 72 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: 0.8254 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 4528 Z= 0.157 Angle : 0.515 8.588 6119 Z= 0.269 Chirality : 0.041 0.135 665 Planarity : 0.004 0.047 800 Dihedral : 4.613 35.027 609 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 0.76 (0.35), residues: 557 helix: 1.76 (0.39), residues: 166 sheet: 0.09 (0.46), residues: 111 loop : -0.01 (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 71 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.564 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 68 average time/residue: 1.1597 time to fit residues: 82.2672 Evaluate side-chains 68 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.7210 time to fit residues: 2.3037 ------------------------------------------------------------------------------- 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: 0.3980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 51 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.8264 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4528 Z= 0.174 Angle : 0.498 8.515 6119 Z= 0.267 Chirality : 0.041 0.135 665 Planarity : 0.004 0.047 800 Dihedral : 4.663 35.232 609 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: 0.83 (0.35), residues: 557 helix: 1.84 (0.39), residues: 166 sheet: 0.12 (0.47), residues: 111 loop : 0.03 (0.38), 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 68 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.485 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 1.1315 time to fit residues: 77.9868 Evaluate side-chains 66 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.572 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.7656 ------------------------------------------------------------------------------- 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: 0.8980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8289 moved from start: 0.2381 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= 0.230 Angle : 0.526 8.655 6119 Z= 0.282 Chirality : 0.042 0.135 665 Planarity : 0.004 0.049 800 Dihedral : 4.818 35.381 609 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.71 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: 0.80 (0.36), residues: 557 helix: 1.76 (0.39), residues: 166 sheet: 0.10 (0.47), residues: 111 loop : 0.05 (0.39), 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 65 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.557 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 64 average time/residue: 1.0867 time to fit residues: 72.7798 Evaluate side-chains 64 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.7396 ------------------------------------------------------------------------------- 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: 0.0970 chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 0.0670 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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: 0.8245 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 4528 Z= 0.146 Angle : 0.475 8.529 6119 Z= 0.254 Chirality : 0.041 0.134 665 Planarity : 0.004 0.047 800 Dihedral : 4.565 34.953 609 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: 0.89 (0.36), residues: 557 helix: 1.98 (0.39), residues: 166 sheet: 0.11 (0.48), residues: 111 loop : 0.02 (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 65 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.611 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 64 average time/residue: 1.0933 time to fit residues: 73.2876 Evaluate side-chains 63 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.7177 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.126599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106132 restraints weight = 5445.891| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.70 r_work: 0.3307 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 1.50 restraints_weight: 0.2500 r_work: 0.3275 rms_B_bonded: 1.57 restraints_weight: 0.1250 r_work: 0.3257 rms_B_bonded: 1.71 restraints_weight: 0.0625 r_work: 0.3238 rms_B_bonded: 1.91 restraints_weight: 0.0312 r_work: 0.3216 rms_B_bonded: 2.17 restraints_weight: 0.0156 r_work: 0.3191 rms_B_bonded: 2.50 restraints_weight: 0.0078 r_work: 0.3164 rms_B_bonded: 2.90 restraints_weight: 0.0039 r_work: 0.3132 rms_B_bonded: 3.40 restraints_weight: 0.0020 r_work: 0.3096 rms_B_bonded: 3.99 restraints_weight: 0.0010 r_work: 0.3055 rms_B_bonded: 4.72 restraints_weight: 0.0005 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2526 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= 0.172 Angle : 0.498 8.524 6119 Z= 0.265 Chirality : 0.041 0.135 665 Planarity : 0.004 0.047 800 Dihedral : 4.591 35.035 609 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: 0.90 (0.36), residues: 557 helix: 1.94 (0.39), residues: 166 sheet: 0.16 (0.48), residues: 111 loop : 0.05 (0.38), residues: 280 =============================================================================== Job complete usr+sys time: 2016.43 seconds wall clock time: 36 minutes 28.19 seconds (2188.19 seconds total)