Starting phenix.real_space_refine on Thu Dec 7 20:38:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/12_2023/6ski_10225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/12_2023/6ski_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_2023/6ski_10225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/12_2023/6ski_10225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/12_2023/6ski_10225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/12_2023/6ski_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.85, 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 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: 1.78 Conformation dependent library (CDL) restraints added in 735.2 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: 0.50 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: 1.19 Time building geometry restraints manager: 1.95 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: 1.820 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: 8.990 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 16.480 Find NCS groups from input model: 0.120 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:10.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- 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 : 0.531 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 1.3007 time to fit residues: 125.3398 Evaluate side-chains 69 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.7172 ------------------------------------------------------------------------------- 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: 0.9980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 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: 0.8006 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4528 Z= 0.251 Angle : 0.605 9.176 6119 Z= 0.317 Chirality : 0.043 0.160 665 Planarity : 0.004 0.050 800 Dihedral : 5.250 29.958 609 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.23 % Allowed : 20.43 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.35), residues: 557 helix: 0.75 (0.38), residues: 165 sheet: 0.30 (0.46), residues: 114 loop : -0.38 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 22 HIS 0.003 0.001 HIS F 14 PHE 0.021 0.001 PHE F 43 TYR 0.010 0.002 TYR F 7 ARG 0.005 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.574 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 82 average time/residue: 1.2716 time to fit residues: 108.1434 Evaluate side-chains 72 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.5681 time to fit residues: 1.9228 ------------------------------------------------------------------------------- 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: 0.0170 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: 5.9990 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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: 0.7985 moved from start: 0.1869 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= 0.191 Angle : 0.546 8.751 6119 Z= 0.287 Chirality : 0.042 0.143 665 Planarity : 0.004 0.048 800 Dihedral : 4.965 32.698 609 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.58 % Allowed : 22.37 % Favored : 75.05 % 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: 0.46 (0.35), residues: 557 helix: 1.16 (0.39), residues: 166 sheet: 0.66 (0.50), residues: 93 loop : -0.24 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 501 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 0.005 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 : 0.497 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 77 average time/residue: 1.1224 time to fit residues: 90.0846 Evaluate side-chains 71 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0448 time to fit residues: 0.8019 ------------------------------------------------------------------------------- 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: 0.4980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4528 Z= 0.294 Angle : 0.571 8.868 6119 Z= 0.304 Chirality : 0.043 0.148 665 Planarity : 0.004 0.050 800 Dihedral : 5.131 34.185 609 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.72 % Allowed : 23.01 % Favored : 75.27 % 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: 0.40 (0.35), residues: 557 helix: 1.15 (0.38), residues: 166 sheet: 0.07 (0.45), residues: 113 loop : -0.09 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 501 HIS 0.004 0.001 HIS F 14 PHE 0.017 0.001 PHE F 43 TYR 0.012 0.002 TYR F 109 ARG 0.005 0.000 ARG F 50 *********************** 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 73 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.537 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 71 average time/residue: 1.1394 time to fit residues: 84.3081 Evaluate side-chains 68 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0432 time to fit residues: 0.7226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8008 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4528 Z= 0.236 Angle : 0.544 8.752 6119 Z= 0.289 Chirality : 0.042 0.144 665 Planarity : 0.004 0.049 800 Dihedral : 4.969 34.768 609 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.80 % Allowed : 22.37 % 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: 0.52 (0.35), residues: 557 helix: 1.32 (0.39), residues: 166 sheet: 0.05 (0.45), residues: 113 loop : -0.02 (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 0.017 0.001 PHE F 43 TYR 0.009 0.001 TYR F 109 ARG 0.006 0.000 ARG F 50 *********************** 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 74 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.514 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 69 average time/residue: 1.1586 time to fit residues: 83.3809 Evaluate side-chains 69 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.3937 time to fit residues: 2.0089 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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: 0.7978 moved from start: 0.2255 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= 0.171 Angle : 0.510 8.594 6119 Z= 0.271 Chirality : 0.041 0.136 665 Planarity : 0.004 0.047 800 Dihedral : 4.730 34.985 609 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.58 % Allowed : 23.01 % 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: 0.70 (0.35), residues: 557 helix: 1.55 (0.39), residues: 166 sheet: 0.05 (0.45), residues: 111 loop : 0.08 (0.39), residues: 280 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 0.006 0.000 ARG F 50 *********************** 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 75 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.503 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 1.1577 time to fit residues: 88.0432 Evaluate side-chains 69 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.0564 time to fit residues: 1.8130 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 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 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: 0.8003 moved from start: 0.2227 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= 0.232 Angle : 0.540 8.655 6119 Z= 0.288 Chirality : 0.042 0.141 665 Planarity : 0.004 0.049 800 Dihedral : 4.854 35.450 609 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.15 % Allowed : 23.23 % 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: 0.72 (0.35), residues: 557 helix: 1.55 (0.38), residues: 166 sheet: 0.08 (0.46), residues: 111 loop : 0.11 (0.39), 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 374 PHE 0.017 0.001 PHE F 43 TYR 0.010 0.001 TYR F 109 ARG 0.007 0.000 ARG F 50 *********************** 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 72 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.548 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 1.2084 time to fit residues: 86.8179 Evaluate side-chains 67 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.0811 time to fit residues: 1.8343 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 49 optimal weight: 0.0470 chunk 51 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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: 0.7976 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4528 Z= 0.171 Angle : 0.513 8.624 6119 Z= 0.272 Chirality : 0.041 0.135 665 Planarity : 0.004 0.047 800 Dihedral : 4.677 35.236 609 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.15 % Allowed : 23.23 % 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: 0.85 (0.35), residues: 557 helix: 1.76 (0.39), residues: 166 sheet: 0.19 (0.46), residues: 113 loop : 0.09 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 22 HIS 0.004 0.001 HIS F 374 PHE 0.019 0.001 PHE F 43 TYR 0.008 0.001 TYR F 480 ARG 0.008 0.000 ARG F 50 *********************** 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 69 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.540 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 67 average time/residue: 1.1190 time to fit residues: 78.3925 Evaluate side-chains 67 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0528 time to fit residues: 0.8527 ------------------------------------------------------------------------------- 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: 0.1980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.0970 chunk 51 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.7971 moved from start: 0.2456 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= 0.165 Angle : 0.487 8.555 6119 Z= 0.261 Chirality : 0.041 0.135 665 Planarity : 0.004 0.047 800 Dihedral : 4.669 35.217 609 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.37 % Allowed : 23.87 % Favored : 73.76 % 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 (0.35), residues: 557 helix: 1.84 (0.39), residues: 166 sheet: 0.20 (0.47), residues: 113 loop : 0.09 (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 374 PHE 0.017 0.001 PHE F 43 TYR 0.008 0.001 TYR F 480 ARG 0.007 0.000 ARG F 50 *********************** 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 70 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.553 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 1.1835 time to fit residues: 81.5191 Evaluate side-chains 67 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.1929 time to fit residues: 1.9981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8008 moved from start: 0.2341 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 : 0.532 8.718 6119 Z= 0.284 Chirality : 0.042 0.137 665 Planarity : 0.004 0.049 800 Dihedral : 4.891 35.355 609 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.72 % Allowed : 24.09 % Favored : 74.19 % 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 (0.36), residues: 557 helix: 1.69 (0.39), residues: 166 sheet: 0.22 (0.47), residues: 113 loop : 0.10 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 501 HIS 0.005 0.001 HIS F 374 PHE 0.016 0.001 PHE F 43 TYR 0.012 0.001 TYR F 109 ARG 0.007 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: 8 poor density : 58 time to evaluate : 0.588 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 65 average time/residue: 1.1406 time to fit residues: 77.4181 Evaluate side-chains 64 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.502 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.7945 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 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 = 0.3489 r_free = 0.3489 target = 0.118123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099008 restraints weight = 5365.553| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.67 r_work: 0.3164 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2359 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= 0.241 Angle : 0.535 8.729 6119 Z= 0.282 Chirality : 0.042 0.139 665 Planarity : 0.004 0.049 800 Dihedral : 4.868 35.280 609 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.15 % Allowed : 23.44 % 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: 0.82 (0.36), residues: 557 helix: 1.70 (0.39), residues: 166 sheet: 0.19 (0.47), residues: 113 loop : 0.09 (0.39), 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 374 PHE 0.017 0.001 PHE F 43 TYR 0.010 0.001 TYR F 109 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: 2185.79 seconds wall clock time: 39 minutes 24.71 seconds (2364.71 seconds total)