Starting phenix.real_space_refine on Sun Mar 10 19:40:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/03_2024/6ski_10225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/03_2024/6ski_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_10225/03_2024/6ski_10225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/03_2024/6ski_10225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/03_2024/6ski_10225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/03_2024/6ski_10225.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 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. Process input model Symmetric amino acids flipped Residue "F ASP 8": "OD1" <-> "OD2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 118": "OD1" <-> "OD2" Residue "F ASP 152": "OD1" <-> "OD2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 163": "OE1" <-> "OE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F ARG 226": "NH1" <-> "NH2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "F TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 342": "OD1" <-> "OD2" Residue "F ASP 343": "OD1" <-> "OD2" Residue "F ARG 345": "NH1" <-> "NH2" Residue "F GLU 408": "OE1" <-> "OE2" Residue "F GLU 430": "OE1" <-> "OE2" Residue "F GLU 450": "OE1" <-> "OE2" Residue "F GLU 476": "OE1" <-> "OE2" Residue "F PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 530": "OD1" <-> "OD2" Residue "F TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A TYR 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 830": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.86, 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: 1.77 Conformation dependent library (CDL) restraints added in 831.4 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: 0.52 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: 1.28 Time building geometry restraints manager: 1.90 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 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.080 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.710 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 % Allowed : 18.06 % Favored : 80.65 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 501 HIS 0.005 0.002 HIS F 310 PHE 0.021 0.002 PHE F 43 TYR 0.013 0.002 TYR F 230 ARG 0.004 0.000 ARG F 96 *********************** 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 : 0.550 Fit side-chains REVERT: F 49 ASN cc_start: 0.8735 (m110) cc_final: 0.8491 (m-40) REVERT: F 50 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7785 (mtt90) REVERT: F 83 LYS cc_start: 0.8556 (mttp) cc_final: 0.8168 (mtpt) REVERT: F 170 GLN cc_start: 0.7913 (tt0) cc_final: 0.7681 (tt0) REVERT: F 397 ILE cc_start: 0.9065 (mm) cc_final: 0.8821 (mm) REVERT: F 453 PHE cc_start: 0.7531 (t80) cc_final: 0.7271 (m-10) REVERT: F 520 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8477 (mtpt) REVERT: A 830 GLU cc_start: 0.7558 (mp0) cc_final: 0.7291 (mp0) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 1.2779 time to fit residues: 123.2065 Evaluate side-chains 72 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 320 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 1.9990 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: 0.9980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 49 ASN F 76 GLN 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1392 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= 0.238 Angle : 0.597 9.098 6119 Z= 0.313 Chirality : 0.043 0.159 665 Planarity : 0.004 0.050 800 Dihedral : 5.332 30.092 612 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.58 % Allowed : 20.65 % Favored : 76.77 % 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: 0.10 (0.35), residues: 557 helix: 0.76 (0.39), residues: 165 sheet: 0.31 (0.46), residues: 114 loop : -0.39 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 501 HIS 0.003 0.001 HIS F 14 PHE 0.020 0.001 PHE F 43 TYR 0.010 0.002 TYR F 230 ARG 0.003 0.000 ARG F 272 *********************** 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: 12 poor density : 76 time to evaluate : 0.464 Fit side-chains REVERT: F 50 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7749 (mtt90) REVERT: F 83 LYS cc_start: 0.8573 (mttp) cc_final: 0.8186 (mtpt) REVERT: F 116 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8101 (mmtm) REVERT: F 170 GLN cc_start: 0.7906 (tt0) cc_final: 0.7702 (tt0) REVERT: F 270 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: F 397 ILE cc_start: 0.9034 (mm) cc_final: 0.8800 (mm) REVERT: F 513 ARG cc_start: 0.8359 (mtm110) cc_final: 0.8129 (mtm-85) REVERT: F 520 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8467 (mtpt) REVERT: A 782 ILE cc_start: 0.6813 (mt) cc_final: 0.6599 (mt) outliers start: 12 outliers final: 5 residues processed: 83 average time/residue: 1.2672 time to fit residues: 109.0075 Evaluate side-chains 76 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 283 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7993 moved from start: 0.1793 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= 0.208 Angle : 0.551 8.787 6119 Z= 0.290 Chirality : 0.042 0.144 665 Planarity : 0.004 0.049 800 Dihedral : 4.990 32.752 609 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.58 % Allowed : 21.08 % Favored : 76.34 % 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: 0.43 (0.35), residues: 557 helix: 1.11 (0.39), residues: 166 sheet: 0.71 (0.50), residues: 93 loop : -0.27 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 22 HIS 0.004 0.001 HIS F 14 PHE 0.018 0.001 PHE F 43 TYR 0.009 0.001 TYR F 480 ARG 0.006 0.000 ARG F 272 *********************** 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 79 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.494 Fit side-chains REVERT: F 83 LYS cc_start: 0.8583 (mttp) cc_final: 0.8204 (mtpt) REVERT: F 116 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8107 (mmtm) REVERT: F 170 GLN cc_start: 0.7917 (tt0) cc_final: 0.7713 (tt0) REVERT: F 397 ILE cc_start: 0.8974 (mm) cc_final: 0.8738 (mm) REVERT: F 520 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8533 (mtpt) REVERT: A 782 ILE cc_start: 0.6774 (mt) cc_final: 0.6568 (mt) outliers start: 12 outliers final: 4 residues processed: 75 average time/residue: 1.2215 time to fit residues: 95.1003 Evaluate side-chains 69 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 320 VAL 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: 0.5980 chunk 54 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8017 moved from start: 0.1949 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= 0.270 Angle : 0.560 8.796 6119 Z= 0.298 Chirality : 0.043 0.147 665 Planarity : 0.004 0.050 800 Dihedral : 5.063 34.196 609 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.51 % Allowed : 22.80 % Favored : 75.70 % 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: 0.41 (0.35), residues: 557 helix: 1.19 (0.38), residues: 166 sheet: 0.14 (0.46), residues: 113 loop : -0.14 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 501 HIS 0.004 0.001 HIS F 14 PHE 0.018 0.001 PHE F 43 TYR 0.010 0.002 TYR F 109 ARG 0.006 0.000 ARG F 272 *********************** 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 71 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.558 Fit side-chains REVERT: F 83 LYS cc_start: 0.8610 (mttp) cc_final: 0.8241 (mtpt) REVERT: F 116 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8182 (mmtm) REVERT: F 170 GLN cc_start: 0.7919 (tt0) cc_final: 0.7716 (tt0) REVERT: F 472 GLN cc_start: 0.7850 (tp40) cc_final: 0.7627 (tp40) REVERT: F 520 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8534 (mtpt) REVERT: A 782 ILE cc_start: 0.6811 (mt) cc_final: 0.6608 (mt) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 1.2484 time to fit residues: 89.6318 Evaluate side-chains 67 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 320 VAL 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: 0.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4528 Z= 0.391 Angle : 0.605 9.057 6119 Z= 0.324 Chirality : 0.044 0.157 665 Planarity : 0.004 0.052 800 Dihedral : 5.297 34.552 609 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.66 % Allowed : 20.65 % Favored : 75.70 % 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: 1.03 (0.38), residues: 166 sheet: 0.03 (0.46), residues: 113 loop : -0.05 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 501 HIS 0.005 0.001 HIS F 14 PHE 0.018 0.002 PHE F 43 TYR 0.013 0.002 TYR F 109 ARG 0.004 0.000 ARG F 272 *********************** 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 79 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.524 Fit side-chains REVERT: F 83 LYS cc_start: 0.8607 (mttp) cc_final: 0.8243 (mtpt) REVERT: F 116 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8224 (mmtm) REVERT: F 117 LYS cc_start: 0.8319 (mttt) cc_final: 0.8099 (mtmm) REVERT: F 170 GLN cc_start: 0.7940 (tt0) cc_final: 0.7721 (tt0) REVERT: F 270 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: F 444 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: F 520 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8527 (mtpt) outliers start: 17 outliers final: 10 residues processed: 72 average time/residue: 1.1465 time to fit residues: 85.9785 Evaluate side-chains 75 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain F residue 449 SER 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: 0.8980 chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.2113 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= 0.204 Angle : 0.532 8.810 6119 Z= 0.283 Chirality : 0.042 0.144 665 Planarity : 0.004 0.049 800 Dihedral : 4.929 34.968 609 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.72 % Allowed : 22.58 % Favored : 75.70 % 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: 0.53 (0.35), residues: 557 helix: 1.36 (0.39), residues: 166 sheet: 0.07 (0.46), residues: 113 loop : -0.05 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 501 HIS 0.005 0.001 HIS F 14 PHE 0.017 0.001 PHE F 43 TYR 0.009 0.001 TYR F 480 ARG 0.004 0.000 ARG F 272 *********************** 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 68 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.522 Fit side-chains REVERT: F 83 LYS cc_start: 0.8616 (mttp) cc_final: 0.8239 (mtpt) REVERT: F 116 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8114 (mmtm) REVERT: F 117 LYS cc_start: 0.8260 (mttt) cc_final: 0.8031 (mtmm) REVERT: F 170 GLN cc_start: 0.7910 (tt0) cc_final: 0.7708 (tt0) REVERT: F 270 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: F 484 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8068 (tttp) REVERT: F 520 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8529 (mtpt) outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 1.2311 time to fit residues: 83.1193 Evaluate side-chains 65 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 484 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 0.0020 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.0470 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 overall best weight: 0.1882 ------------------------------------------------------------------------------- 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: 0.7932 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4528 Z= 0.121 Angle : 0.495 8.506 6119 Z= 0.260 Chirality : 0.041 0.131 665 Planarity : 0.004 0.046 800 Dihedral : 4.505 34.868 609 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.94 % Allowed : 22.15 % Favored : 75.91 % 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: 1.83 (0.39), residues: 166 sheet: 0.11 (0.46), residues: 111 loop : -0.04 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 22 HIS 0.004 0.001 HIS F 14 PHE 0.018 0.001 PHE F 43 TYR 0.010 0.001 TYR F 480 ARG 0.006 0.000 ARG F 272 *********************** 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 76 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.550 Fit side-chains REVERT: F 14 HIS cc_start: 0.6721 (t-170) cc_final: 0.6483 (t70) REVERT: F 83 LYS cc_start: 0.8577 (mttp) cc_final: 0.8187 (mtpt) REVERT: F 170 GLN cc_start: 0.7916 (tt0) cc_final: 0.7701 (tt0) REVERT: F 300 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6247 (tpt) REVERT: F 520 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8549 (mtpt) outliers start: 9 outliers final: 1 residues processed: 73 average time/residue: 1.2519 time to fit residues: 94.8929 Evaluate side-chains 63 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 300 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 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 387 ASN A 791 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4528 Z= 0.227 Angle : 0.532 8.600 6119 Z= 0.284 Chirality : 0.042 0.136 665 Planarity : 0.004 0.048 800 Dihedral : 4.765 35.152 609 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.29 % Allowed : 23.87 % Favored : 74.84 % 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: 0.81 (0.35), residues: 557 helix: 1.72 (0.39), residues: 166 sheet: 0.22 (0.46), residues: 113 loop : 0.03 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 22 HIS 0.005 0.001 HIS F 14 PHE 0.018 0.001 PHE F 43 TYR 0.010 0.002 TYR F 290 ARG 0.007 0.000 ARG F 272 *********************** 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 67 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.522 Fit side-chains REVERT: F 83 LYS cc_start: 0.8618 (mttp) cc_final: 0.8235 (mtpt) REVERT: F 116 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8127 (mmtm) REVERT: F 117 LYS cc_start: 0.8289 (mttp) cc_final: 0.8033 (mtmm) REVERT: F 170 GLN cc_start: 0.7935 (tt0) cc_final: 0.7723 (tt0) REVERT: F 520 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8533 (mtpt) outliers start: 6 outliers final: 3 residues processed: 65 average time/residue: 1.2411 time to fit residues: 83.7862 Evaluate side-chains 64 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 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 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: 0.7992 moved from start: 0.2328 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= 0.213 Angle : 0.524 8.687 6119 Z= 0.280 Chirality : 0.042 0.135 665 Planarity : 0.004 0.048 800 Dihedral : 4.758 35.208 609 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.29 % Allowed : 24.30 % Favored : 74.41 % 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: 1.73 (0.39), residues: 166 sheet: 0.24 (0.47), residues: 113 loop : 0.06 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 22 HIS 0.005 0.001 HIS F 14 PHE 0.018 0.001 PHE F 43 TYR 0.009 0.001 TYR F 109 ARG 0.007 0.000 ARG F 272 *********************** 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 66 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.539 Fit side-chains REVERT: F 14 HIS cc_start: 0.6659 (t-170) cc_final: 0.6450 (t70) REVERT: F 83 LYS cc_start: 0.8613 (mttp) cc_final: 0.8234 (mtpt) REVERT: F 116 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8100 (mmtm) REVERT: F 117 LYS cc_start: 0.8265 (mttp) cc_final: 0.8012 (mtmm) REVERT: F 170 GLN cc_start: 0.7919 (tt0) cc_final: 0.7713 (tt0) REVERT: F 183 ASP cc_start: 0.7837 (t0) cc_final: 0.7565 (t0) REVERT: F 520 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8534 (mtpt) outliers start: 6 outliers final: 4 residues processed: 64 average time/residue: 1.2918 time to fit residues: 85.9112 Evaluate side-chains 64 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 320 VAL 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: 0.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.2302 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= 0.257 Angle : 0.541 8.708 6119 Z= 0.290 Chirality : 0.042 0.140 665 Planarity : 0.004 0.049 800 Dihedral : 4.890 35.263 609 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.29 % Allowed : 24.09 % Favored : 74.62 % 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 (0.36), residues: 557 helix: 1.65 (0.39), residues: 166 sheet: 0.19 (0.47), residues: 113 loop : 0.06 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 501 HIS 0.006 0.001 HIS F 14 PHE 0.017 0.001 PHE F 43 TYR 0.011 0.001 TYR F 109 ARG 0.006 0.000 ARG F 272 ********************** 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 66 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.509 Fit side-chains REVERT: F 83 LYS cc_start: 0.8611 (mttp) cc_final: 0.8236 (mtpt) REVERT: F 116 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8141 (mmtm) REVERT: F 117 LYS cc_start: 0.8289 (mttp) cc_final: 0.8052 (mtmm) REVERT: F 183 ASP cc_start: 0.7739 (t0) cc_final: 0.7448 (t0) REVERT: F 520 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8535 (mtpt) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 1.2306 time to fit residues: 83.1636 Evaluate side-chains 66 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.119048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099887 restraints weight = 5347.056| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.66 r_work: 0.3179 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4528 Z= 0.199 Angle : 0.528 8.733 6119 Z= 0.278 Chirality : 0.042 0.137 665 Planarity : 0.004 0.048 800 Dihedral : 4.747 35.259 609 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.72 % Allowed : 23.66 % Favored : 74.62 % 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: 0.82 (0.36), residues: 557 helix: 1.76 (0.39), residues: 166 sheet: 0.20 (0.48), residues: 113 loop : 0.04 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 22 HIS 0.006 0.001 HIS F 14 PHE 0.018 0.001 PHE F 43 TYR 0.008 0.001 TYR F 7 ARG 0.007 0.000 ARG F 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2207.82 seconds wall clock time: 39 minutes 36.68 seconds (2376.68 seconds total)