Starting phenix.real_space_refine on Sun Mar 10 22:54:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/03_2024/8ej5_28176.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/03_2024/8ej5_28176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/03_2024/8ej5_28176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/03_2024/8ej5_28176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/03_2024/8ej5_28176.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/03_2024/8ej5_28176.pdb" } resolution = 4.9 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= 0.003 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 17 5.16 5 C 3712 2.51 5 N 981 2.21 5 O 1108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 5": "OE1" <-> "OE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5818 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3556 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 435} Chain breaks: 1 Chain: "B" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "C" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Time building chain proxies: 3.58, per 1000 atoms: 0.62 Number of scatterers: 5818 At special positions: 0 Unit cell: (74.368, 95.616, 131.472, 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 17 16.00 O 1108 8.00 N 981 7.00 C 3712 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: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 59.3% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 22 through 30 removed outlier: 4.300A pdb=" N GLY A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 43 through 58 Processing helix chain 'A' and resid 60 through 72 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 123 through 137 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.151A pdb=" N TRP A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.513A pdb=" N LEU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 353 through 367 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.662A pdb=" N VAL A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'B' and resid 2 through 21 removed outlier: 3.824A pdb=" N GLN B 21 " --> pdb=" O ASN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 45 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.529A pdb=" N TYR B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 86 Processing helix chain 'C' and resid 2 through 21 removed outlier: 3.825A pdb=" N GLN C 21 " --> pdb=" O ASN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.526A pdb=" N TYR C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'D' and resid 2 through 21 removed outlier: 3.806A pdb=" N GLN D 21 " --> pdb=" O ASN D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 45 Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 61 through 68 removed outlier: 3.527A pdb=" N TYR D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 86 Processing sheet with id=AA1, first strand: chain 'A' and resid 249 through 255 removed outlier: 6.199A pdb=" N THR A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 317 removed outlier: 5.139A pdb=" N GLY A 315 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 454 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 434 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 422 " --> pdb=" O PHE A 404 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 906 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: 1.41 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1171 1.32 - 1.45: 1552 1.45 - 1.57: 3214 1.57 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 5966 Sorted by residual: bond pdb=" N VAL A 394 " pdb=" CA VAL A 394 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N VAL A 440 " pdb=" CA VAL A 440 " ideal model delta sigma weight residual 1.462 1.492 -0.031 8.70e-03 1.32e+04 1.23e+01 bond pdb=" N VAL A 425 " pdb=" CA VAL A 425 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.22e+01 bond pdb=" N VAL A 427 " pdb=" CA VAL A 427 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.22e+01 bond pdb=" N GLU D 47 " pdb=" CA GLU D 47 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.07e+01 ... (remaining 5961 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.55: 171 106.55 - 113.78: 3065 113.78 - 121.02: 2861 121.02 - 128.26: 1954 128.26 - 135.49: 49 Bond angle restraints: 8100 Sorted by residual: angle pdb=" CA GLY A 314 " pdb=" C GLY A 314 " pdb=" N GLY A 315 " ideal model delta sigma weight residual 115.11 120.97 -5.86 9.50e-01 1.11e+00 3.81e+01 angle pdb=" N GLY A 315 " pdb=" CA GLY A 315 " pdb=" C GLY A 315 " ideal model delta sigma weight residual 110.56 118.63 -8.07 1.36e+00 5.41e-01 3.52e+01 angle pdb=" N ASN A 284 " pdb=" CA ASN A 284 " pdb=" C ASN A 284 " ideal model delta sigma weight residual 111.54 104.26 7.28 1.36e+00 5.41e-01 2.87e+01 angle pdb=" N LYS A 272 " pdb=" CA LYS A 272 " pdb=" C LYS A 272 " ideal model delta sigma weight residual 111.28 105.48 5.80 1.09e+00 8.42e-01 2.83e+01 angle pdb=" CA LYS A 242 " pdb=" C LYS A 242 " pdb=" O LYS A 242 " ideal model delta sigma weight residual 120.63 114.92 5.71 1.08e+00 8.57e-01 2.80e+01 ... (remaining 8095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3161 16.49 - 32.97: 214 32.97 - 49.46: 63 49.46 - 65.95: 11 65.95 - 82.44: 3 Dihedral angle restraints: 3452 sinusoidal: 1360 harmonic: 2092 Sorted by residual: dihedral pdb=" C ASN A 316 " pdb=" N ASN A 316 " pdb=" CA ASN A 316 " pdb=" CB ASN A 316 " ideal model delta harmonic sigma weight residual -122.60 -133.15 10.55 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" N ASN A 465 " pdb=" CA ASN A 465 " pdb=" CB ASN A 465 " pdb=" CG ASN A 465 " ideal model delta sinusoidal sigma weight residual -180.00 -125.56 -54.44 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA ILE A 275 " pdb=" CB ILE A 275 " pdb=" CG1 ILE A 275 " pdb=" CD1 ILE A 275 " ideal model delta sinusoidal sigma weight residual -180.00 -127.13 -52.87 3 1.50e+01 4.44e-03 9.15e+00 ... (remaining 3449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 366 0.067 - 0.135: 376 0.135 - 0.202: 85 0.202 - 0.270: 6 0.270 - 0.337: 2 Chirality restraints: 835 Sorted by residual: chirality pdb=" CA ILE A 251 " pdb=" N ILE A 251 " pdb=" C ILE A 251 " pdb=" CB ILE A 251 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ILE A 238 " pdb=" N ILE A 238 " pdb=" C ILE A 238 " pdb=" CB ILE A 238 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASN A 316 " pdb=" N ASN A 316 " pdb=" C ASN A 316 " pdb=" CB ASN A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 832 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 84 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C SER A 84 " 0.064 2.00e-02 2.50e+03 pdb=" O SER A 84 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO A 85 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 78 " 0.045 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR D 78 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR D 78 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR D 78 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR D 78 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 78 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 78 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 78 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 78 " 0.042 2.00e-02 2.50e+03 2.19e-02 9.62e+00 pdb=" CG TYR B 78 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 78 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 78 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 78 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 78 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 78 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 78 " 0.019 2.00e-02 2.50e+03 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 2740 2.96 - 3.44: 6379 3.44 - 3.93: 10549 3.93 - 4.41: 11549 4.41 - 4.90: 18520 Nonbonded interactions: 49737 Sorted by model distance: nonbonded pdb=" O SER A 84 " pdb=" OE1 GLU B 58 " model vdw 2.472 3.040 nonbonded pdb=" O ARG A 311 " pdb=" N ASP A 456 " model vdw 2.478 2.520 nonbonded pdb=" N PHE A 244 " pdb=" O ILE A 251 " model vdw 2.487 2.520 nonbonded pdb=" O GLY A 281 " pdb=" OD1 ASP A 464 " model vdw 2.488 3.040 nonbonded pdb=" N THR A 318 " pdb=" OD1 ASN A 321 " model vdw 2.490 2.520 ... (remaining 49732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 3.740 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.920 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 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 : 0.012 0.047 5966 Z= 0.776 Angle : 1.519 9.118 8100 Z= 1.153 Chirality : 0.090 0.337 835 Planarity : 0.010 0.109 1071 Dihedral : 12.691 82.437 2124 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.84 % Allowed : 1.95 % Favored : 97.21 % Rotamer: Outliers : 3.27 % Allowed : 4.91 % Favored : 91.82 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 8.33 % 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: 1.40 (0.30), residues: 717 helix: 1.44 (0.25), residues: 397 sheet: 0.11 (0.71), residues: 42 loop : 0.49 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.006 TRP A 79 HIS 0.019 0.004 HIS C 88 PHE 0.024 0.004 PHE B 77 TYR 0.045 0.005 TYR D 78 ARG 0.008 0.002 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 328 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7439 (ttm) cc_final: 0.6453 (ttm) REVERT: A 33 ILE cc_start: 0.6295 (mt) cc_final: 0.6059 (mt) REVERT: A 74 ASN cc_start: 0.6556 (t0) cc_final: 0.4873 (t0) REVERT: A 80 LEU cc_start: 0.8388 (tp) cc_final: 0.8181 (tp) REVERT: A 176 ASN cc_start: 0.9194 (t0) cc_final: 0.8478 (p0) REVERT: A 179 LEU cc_start: 0.8689 (tp) cc_final: 0.7989 (tp) REVERT: A 229 ASP cc_start: 0.8564 (m-30) cc_final: 0.8296 (m-30) REVERT: A 234 ASP cc_start: 0.8173 (m-30) cc_final: 0.7842 (t0) REVERT: A 241 ASP cc_start: 0.8580 (m-30) cc_final: 0.8082 (p0) REVERT: A 322 LEU cc_start: 0.8657 (tp) cc_final: 0.8281 (tp) REVERT: A 335 PHE cc_start: 0.7934 (t80) cc_final: 0.7420 (t80) REVERT: A 350 ASP cc_start: 0.8412 (m-30) cc_final: 0.7843 (m-30) REVERT: A 357 LEU cc_start: 0.9093 (tp) cc_final: 0.8798 (tp) REVERT: A 361 TYR cc_start: 0.8506 (t80) cc_final: 0.8182 (t80) REVERT: A 362 MET cc_start: 0.9093 (mmm) cc_final: 0.8638 (mmt) REVERT: A 363 HIS cc_start: 0.8420 (t-170) cc_final: 0.8072 (t70) REVERT: A 366 TRP cc_start: 0.7592 (m100) cc_final: 0.7165 (m100) REVERT: A 412 GLN cc_start: 0.8505 (mt0) cc_final: 0.8260 (mt0) REVERT: A 438 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6783 (m-10) REVERT: A 439 ASN cc_start: 0.8977 (t0) cc_final: 0.8442 (t0) REVERT: A 455 ILE cc_start: 0.8795 (mm) cc_final: 0.8249 (mp) REVERT: A 469 PHE cc_start: 0.8974 (p90) cc_final: 0.8695 (p90) REVERT: B 19 LEU cc_start: 0.8990 (mt) cc_final: 0.8728 (mt) REVERT: B 89 ILE cc_start: 0.5995 (pt) cc_final: 0.5415 (pt) REVERT: C 12 MET cc_start: 0.8845 (tpt) cc_final: 0.8053 (tpt) REVERT: C 19 LEU cc_start: 0.9480 (mt) cc_final: 0.9270 (mt) REVERT: C 36 VAL cc_start: 0.9385 (t) cc_final: 0.9032 (m) REVERT: C 38 CYS cc_start: 0.9134 (m) cc_final: 0.7947 (t) REVERT: C 42 LEU cc_start: 0.8909 (mt) cc_final: 0.6001 (mt) REVERT: C 62 LEU cc_start: 0.9434 (tp) cc_final: 0.9090 (tp) REVERT: C 77 PHE cc_start: 0.8051 (t80) cc_final: 0.7832 (t80) REVERT: C 82 TYR cc_start: 0.8394 (t80) cc_final: 0.7898 (t80) REVERT: D 15 LEU cc_start: 0.9449 (tp) cc_final: 0.9114 (tp) REVERT: D 17 ASN cc_start: 0.8021 (m-40) cc_final: 0.7456 (m110) REVERT: D 19 LEU cc_start: 0.9459 (mt) cc_final: 0.9172 (mt) REVERT: D 66 LEU cc_start: 0.8729 (mt) cc_final: 0.8485 (mt) REVERT: D 74 GLN cc_start: 0.8940 (mt0) cc_final: 0.8290 (mm-40) outliers start: 20 outliers final: 5 residues processed: 333 average time/residue: 0.1901 time to fit residues: 79.4705 Evaluate side-chains 197 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.0770 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN A 412 GLN C 20 GLN C 32 ASN D 32 ASN D 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5966 Z= 0.195 Angle : 0.637 9.638 8100 Z= 0.337 Chirality : 0.044 0.252 835 Planarity : 0.006 0.139 1071 Dihedral : 5.676 86.331 784 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.95 % Favored : 97.77 % Rotamer: Outliers : 0.16 % Allowed : 1.80 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.72 (0.32), residues: 717 helix: 1.86 (0.26), residues: 402 sheet: 0.43 (0.72), residues: 44 loop : 0.29 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 156 HIS 0.004 0.001 HIS A 396 PHE 0.024 0.002 PHE A 244 TYR 0.016 0.002 TYR D 78 ARG 0.007 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.6933 (t0) cc_final: 0.6429 (t0) REVERT: A 137 ASN cc_start: 0.7654 (t0) cc_final: 0.7341 (t0) REVERT: A 176 ASN cc_start: 0.9189 (t0) cc_final: 0.8463 (p0) REVERT: A 179 LEU cc_start: 0.8656 (tp) cc_final: 0.7979 (tp) REVERT: A 248 MET cc_start: 0.9112 (mpp) cc_final: 0.8669 (mpp) REVERT: A 278 ILE cc_start: 0.8518 (mp) cc_final: 0.8025 (tt) REVERT: A 330 ILE cc_start: 0.7993 (mt) cc_final: 0.7609 (mt) REVERT: A 383 VAL cc_start: 0.9543 (p) cc_final: 0.9316 (p) REVERT: A 394 VAL cc_start: 0.8000 (t) cc_final: 0.7548 (t) REVERT: A 439 ASN cc_start: 0.9275 (t0) cc_final: 0.8411 (t0) REVERT: A 440 VAL cc_start: 0.9506 (m) cc_final: 0.9066 (m) REVERT: B 19 LEU cc_start: 0.8493 (mt) cc_final: 0.8191 (mt) REVERT: C 4 GLU cc_start: 0.8141 (mp0) cc_final: 0.7532 (tm-30) REVERT: C 9 TYR cc_start: 0.7665 (m-10) cc_final: 0.7308 (m-10) REVERT: C 12 MET cc_start: 0.8890 (tpt) cc_final: 0.8415 (ptt) REVERT: C 16 PHE cc_start: 0.9243 (t80) cc_final: 0.9006 (t80) REVERT: C 27 THR cc_start: 0.8360 (m) cc_final: 0.8039 (m) REVERT: C 52 PHE cc_start: 0.9043 (t80) cc_final: 0.8632 (t80) REVERT: C 55 ASP cc_start: 0.7959 (t70) cc_final: 0.7473 (t0) REVERT: C 62 LEU cc_start: 0.9471 (tp) cc_final: 0.9221 (tp) REVERT: C 82 TYR cc_start: 0.8807 (t80) cc_final: 0.8260 (t80) REVERT: D 15 LEU cc_start: 0.9299 (tp) cc_final: 0.8930 (tp) REVERT: D 17 ASN cc_start: 0.8603 (m-40) cc_final: 0.7964 (m110) REVERT: D 19 LEU cc_start: 0.9301 (mt) cc_final: 0.8905 (mt) REVERT: D 33 ASN cc_start: 0.8948 (m110) cc_final: 0.8561 (m110) REVERT: D 59 ASP cc_start: 0.9171 (m-30) cc_final: 0.8829 (m-30) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.1578 time to fit residues: 50.3091 Evaluate side-chains 185 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 0.0170 chunk 64 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 236 HIS C 20 GLN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5966 Z= 0.165 Angle : 0.584 8.593 8100 Z= 0.304 Chirality : 0.042 0.202 835 Planarity : 0.004 0.038 1071 Dihedral : 4.826 43.083 784 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.95 % Favored : 97.77 % Rotamer: Outliers : 0.33 % Allowed : 1.80 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.32 (0.32), residues: 717 helix: 1.46 (0.26), residues: 401 sheet: 0.60 (0.72), residues: 44 loop : 0.18 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 22 HIS 0.005 0.001 HIS A 12 PHE 0.022 0.002 PHE C 25 TYR 0.015 0.001 TYR D 78 ARG 0.008 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7727 (m-80) cc_final: 0.7445 (m-80) REVERT: A 80 LEU cc_start: 0.8930 (tp) cc_final: 0.8726 (tp) REVERT: A 92 ASP cc_start: 0.6784 (t0) cc_final: 0.6559 (t0) REVERT: A 137 ASN cc_start: 0.7432 (t0) cc_final: 0.6913 (t0) REVERT: A 138 MET cc_start: 0.6868 (mmp) cc_final: 0.6525 (mmm) REVERT: A 176 ASN cc_start: 0.9124 (t0) cc_final: 0.8514 (p0) REVERT: A 270 GLU cc_start: 0.8199 (tp30) cc_final: 0.7826 (tp30) REVERT: A 278 ILE cc_start: 0.8781 (mp) cc_final: 0.8507 (mm) REVERT: A 322 LEU cc_start: 0.8699 (tp) cc_final: 0.8327 (tp) REVERT: A 330 ILE cc_start: 0.7973 (mt) cc_final: 0.7677 (mt) REVERT: A 357 LEU cc_start: 0.8884 (tp) cc_final: 0.8648 (tp) REVERT: A 384 TRP cc_start: 0.9252 (p-90) cc_final: 0.8485 (p-90) REVERT: A 439 ASN cc_start: 0.9319 (t0) cc_final: 0.8353 (t0) REVERT: A 464 ASP cc_start: 0.8154 (p0) cc_final: 0.7760 (p0) REVERT: A 469 PHE cc_start: 0.8623 (p90) cc_final: 0.8305 (p90) REVERT: B 19 LEU cc_start: 0.8325 (mt) cc_final: 0.7823 (mt) REVERT: B 24 ASP cc_start: 0.7556 (t0) cc_final: 0.6915 (t0) REVERT: C 4 GLU cc_start: 0.8711 (mp0) cc_final: 0.7621 (tm-30) REVERT: C 9 TYR cc_start: 0.7616 (m-10) cc_final: 0.7268 (m-10) REVERT: C 16 PHE cc_start: 0.9288 (t80) cc_final: 0.8994 (t80) REVERT: C 24 ASP cc_start: 0.7977 (t70) cc_final: 0.7619 (t0) REVERT: C 27 THR cc_start: 0.8472 (m) cc_final: 0.8039 (m) REVERT: C 55 ASP cc_start: 0.7890 (t70) cc_final: 0.7648 (t0) REVERT: C 82 TYR cc_start: 0.8948 (t80) cc_final: 0.8558 (t80) REVERT: D 15 LEU cc_start: 0.9300 (tp) cc_final: 0.9034 (tp) REVERT: D 17 ASN cc_start: 0.8634 (m-40) cc_final: 0.8007 (m110) REVERT: D 18 LEU cc_start: 0.9637 (mm) cc_final: 0.9404 (mm) REVERT: D 33 ASN cc_start: 0.8757 (m110) cc_final: 0.8310 (m110) REVERT: D 50 ILE cc_start: 0.8749 (tp) cc_final: 0.8519 (mt) REVERT: D 59 ASP cc_start: 0.9237 (m-30) cc_final: 0.8911 (m-30) REVERT: D 66 LEU cc_start: 0.9014 (mt) cc_final: 0.8717 (mt) REVERT: D 70 ASP cc_start: 0.8664 (t70) cc_final: 0.7311 (t0) REVERT: D 74 GLN cc_start: 0.8580 (mt0) cc_final: 0.8030 (mm-40) REVERT: D 89 ILE cc_start: 0.8211 (pt) cc_final: 0.7737 (pt) outliers start: 2 outliers final: 1 residues processed: 231 average time/residue: 0.1693 time to fit residues: 51.8615 Evaluate side-chains 178 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5966 Z= 0.153 Angle : 0.570 9.520 8100 Z= 0.292 Chirality : 0.040 0.170 835 Planarity : 0.004 0.042 1071 Dihedral : 4.551 38.836 784 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.81 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.31 (0.32), residues: 717 helix: 1.45 (0.26), residues: 405 sheet: 0.00 (0.69), residues: 50 loop : 0.27 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 156 HIS 0.003 0.001 HIS A 12 PHE 0.013 0.001 PHE C 25 TYR 0.023 0.001 TYR B 65 ARG 0.005 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7711 (m-80) cc_final: 0.7376 (m-80) REVERT: A 92 ASP cc_start: 0.6902 (t0) cc_final: 0.6630 (t0) REVERT: A 137 ASN cc_start: 0.7582 (t0) cc_final: 0.6849 (t0) REVERT: A 138 MET cc_start: 0.7090 (mmp) cc_final: 0.6802 (mmm) REVERT: A 176 ASN cc_start: 0.9119 (t0) cc_final: 0.8586 (p0) REVERT: A 322 LEU cc_start: 0.8640 (tp) cc_final: 0.8263 (tp) REVERT: A 330 ILE cc_start: 0.8052 (mt) cc_final: 0.7730 (mt) REVERT: A 331 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7681 (mm-30) REVERT: A 357 LEU cc_start: 0.8890 (tp) cc_final: 0.8503 (tp) REVERT: A 437 ASN cc_start: 0.8789 (p0) cc_final: 0.7797 (p0) REVERT: A 439 ASN cc_start: 0.9230 (t0) cc_final: 0.8246 (t0) REVERT: A 451 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 469 PHE cc_start: 0.8611 (p90) cc_final: 0.8339 (p90) REVERT: B 19 LEU cc_start: 0.8329 (mt) cc_final: 0.8062 (mt) REVERT: B 24 ASP cc_start: 0.7370 (t0) cc_final: 0.5184 (t0) REVERT: B 62 LEU cc_start: 0.8543 (tp) cc_final: 0.8217 (tp) REVERT: C 4 GLU cc_start: 0.8783 (mp0) cc_final: 0.7781 (tm-30) REVERT: C 5 LYS cc_start: 0.8554 (pttp) cc_final: 0.8354 (pttp) REVERT: C 9 TYR cc_start: 0.8293 (m-10) cc_final: 0.7848 (m-10) REVERT: C 12 MET cc_start: 0.9148 (tpt) cc_final: 0.8699 (ttp) REVERT: C 16 PHE cc_start: 0.9318 (t80) cc_final: 0.8886 (t80) REVERT: C 27 THR cc_start: 0.8490 (m) cc_final: 0.7612 (m) REVERT: C 41 LEU cc_start: 0.9537 (mt) cc_final: 0.9309 (mt) REVERT: C 55 ASP cc_start: 0.7987 (t70) cc_final: 0.7599 (t0) REVERT: C 82 TYR cc_start: 0.9028 (t80) cc_final: 0.8725 (t80) REVERT: D 13 LEU cc_start: 0.9015 (tt) cc_final: 0.8373 (tt) REVERT: D 16 PHE cc_start: 0.9221 (t80) cc_final: 0.8909 (t80) REVERT: D 17 ASN cc_start: 0.8870 (m-40) cc_final: 0.8461 (m110) REVERT: D 18 LEU cc_start: 0.9682 (mm) cc_final: 0.9394 (mm) REVERT: D 33 ASN cc_start: 0.8853 (m110) cc_final: 0.8371 (m110) REVERT: D 35 LEU cc_start: 0.9390 (mm) cc_final: 0.9137 (mm) REVERT: D 59 ASP cc_start: 0.9294 (m-30) cc_final: 0.9070 (m-30) REVERT: D 66 LEU cc_start: 0.9136 (mt) cc_final: 0.8832 (mt) REVERT: D 74 GLN cc_start: 0.8628 (mt0) cc_final: 0.7974 (mm-40) REVERT: D 89 ILE cc_start: 0.8282 (pt) cc_final: 0.7932 (pt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1492 time to fit residues: 44.5681 Evaluate side-chains 172 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 0.0270 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS B 33 ASN ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5966 Z= 0.177 Angle : 0.590 9.833 8100 Z= 0.306 Chirality : 0.040 0.169 835 Planarity : 0.003 0.035 1071 Dihedral : 4.385 31.275 784 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.79 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.41 (0.32), residues: 717 helix: 1.52 (0.27), residues: 400 sheet: 0.71 (0.72), residues: 44 loop : 0.24 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 22 HIS 0.006 0.001 HIS A 236 PHE 0.018 0.002 PHE C 90 TYR 0.013 0.001 TYR A 438 ARG 0.003 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7734 (m-80) cc_final: 0.7350 (m-80) REVERT: A 77 TRP cc_start: 0.7072 (m-90) cc_final: 0.6747 (m-90) REVERT: A 92 ASP cc_start: 0.7059 (t0) cc_final: 0.6819 (t0) REVERT: A 137 ASN cc_start: 0.7719 (t0) cc_final: 0.6956 (t0) REVERT: A 138 MET cc_start: 0.7178 (mmp) cc_final: 0.6956 (mmm) REVERT: A 176 ASN cc_start: 0.9212 (t0) cc_final: 0.8417 (p0) REVERT: A 270 GLU cc_start: 0.7831 (tp30) cc_final: 0.7408 (tp30) REVERT: A 322 LEU cc_start: 0.8645 (tp) cc_final: 0.8368 (tp) REVERT: A 357 LEU cc_start: 0.8951 (tp) cc_final: 0.8564 (tp) REVERT: A 412 GLN cc_start: 0.9099 (mt0) cc_final: 0.8798 (mt0) REVERT: A 437 ASN cc_start: 0.8699 (p0) cc_final: 0.7698 (p0) REVERT: A 439 ASN cc_start: 0.8997 (t0) cc_final: 0.8217 (t0) REVERT: A 451 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7570 (mt-10) REVERT: A 464 ASP cc_start: 0.8068 (p0) cc_final: 0.7718 (p0) REVERT: B 19 LEU cc_start: 0.8382 (mt) cc_final: 0.7663 (mt) REVERT: B 24 ASP cc_start: 0.7650 (t0) cc_final: 0.6500 (t0) REVERT: C 4 GLU cc_start: 0.8825 (mp0) cc_final: 0.7958 (tm-30) REVERT: C 9 TYR cc_start: 0.8533 (m-10) cc_final: 0.8151 (m-10) REVERT: C 16 PHE cc_start: 0.9355 (t80) cc_final: 0.8828 (t80) REVERT: C 22 TRP cc_start: 0.7930 (m100) cc_final: 0.7604 (m-10) REVERT: C 27 THR cc_start: 0.8411 (m) cc_final: 0.7864 (m) REVERT: C 41 LEU cc_start: 0.9525 (mt) cc_final: 0.9248 (mt) REVERT: C 55 ASP cc_start: 0.8017 (t70) cc_final: 0.7599 (t0) REVERT: C 86 ASN cc_start: 0.8794 (m-40) cc_final: 0.8499 (p0) REVERT: C 89 ILE cc_start: 0.8287 (mp) cc_final: 0.7411 (mp) REVERT: D 13 LEU cc_start: 0.9007 (tt) cc_final: 0.8469 (tt) REVERT: D 15 LEU cc_start: 0.9484 (tp) cc_final: 0.9048 (tp) REVERT: D 16 PHE cc_start: 0.9143 (t80) cc_final: 0.8835 (t80) REVERT: D 17 ASN cc_start: 0.9006 (m-40) cc_final: 0.8471 (m110) REVERT: D 18 LEU cc_start: 0.9706 (mm) cc_final: 0.9374 (mm) REVERT: D 19 LEU cc_start: 0.9159 (mt) cc_final: 0.8842 (mt) REVERT: D 35 LEU cc_start: 0.9409 (mm) cc_final: 0.9094 (mm) REVERT: D 42 LEU cc_start: 0.9073 (mt) cc_final: 0.8648 (mt) REVERT: D 59 ASP cc_start: 0.9320 (m-30) cc_final: 0.9095 (m-30) REVERT: D 62 LEU cc_start: 0.9662 (tp) cc_final: 0.9269 (tp) REVERT: D 66 LEU cc_start: 0.9330 (mt) cc_final: 0.8996 (mt) REVERT: D 74 GLN cc_start: 0.8643 (mt0) cc_final: 0.7828 (mm-40) REVERT: D 81 PHE cc_start: 0.7573 (t80) cc_final: 0.7181 (t80) REVERT: D 89 ILE cc_start: 0.8339 (pt) cc_final: 0.7529 (mp) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1525 time to fit residues: 43.8241 Evaluate side-chains 173 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.7384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5966 Z= 0.179 Angle : 0.603 8.364 8100 Z= 0.313 Chirality : 0.040 0.180 835 Planarity : 0.003 0.033 1071 Dihedral : 4.516 32.515 784 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.79 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.20 (0.32), residues: 717 helix: 1.41 (0.27), residues: 400 sheet: 0.87 (0.74), residues: 42 loop : -0.02 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 156 HIS 0.004 0.001 HIS B 88 PHE 0.012 0.001 PHE D 25 TYR 0.018 0.002 TYR D 82 ARG 0.002 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7963 (m-80) cc_final: 0.7566 (m-80) REVERT: A 77 TRP cc_start: 0.7099 (m-90) cc_final: 0.6845 (m-90) REVERT: A 92 ASP cc_start: 0.6780 (t0) cc_final: 0.6571 (t0) REVERT: A 137 ASN cc_start: 0.7811 (t0) cc_final: 0.7030 (t0) REVERT: A 176 ASN cc_start: 0.9227 (t0) cc_final: 0.8459 (p0) REVERT: A 270 GLU cc_start: 0.8111 (tp30) cc_final: 0.7431 (tp30) REVERT: A 271 MET cc_start: 0.8519 (mmp) cc_final: 0.7941 (mmm) REVERT: A 322 LEU cc_start: 0.8709 (tp) cc_final: 0.8371 (tp) REVERT: A 357 LEU cc_start: 0.9077 (tp) cc_final: 0.8725 (tp) REVERT: A 412 GLN cc_start: 0.9048 (mt0) cc_final: 0.8703 (mt0) REVERT: A 437 ASN cc_start: 0.8806 (p0) cc_final: 0.7793 (p0) REVERT: A 439 ASN cc_start: 0.9227 (t0) cc_final: 0.8412 (t0) REVERT: A 451 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 464 ASP cc_start: 0.7429 (p0) cc_final: 0.7136 (p0) REVERT: B 24 ASP cc_start: 0.7228 (t0) cc_final: 0.5763 (t0) REVERT: B 33 ASN cc_start: 0.9123 (m-40) cc_final: 0.8864 (m110) REVERT: C 4 GLU cc_start: 0.8761 (mp0) cc_final: 0.7827 (tm-30) REVERT: C 16 PHE cc_start: 0.9370 (t80) cc_final: 0.8894 (t80) REVERT: C 27 THR cc_start: 0.8596 (m) cc_final: 0.7141 (m) REVERT: C 34 LEU cc_start: 0.9088 (tp) cc_final: 0.8885 (tp) REVERT: C 41 LEU cc_start: 0.9523 (mt) cc_final: 0.9226 (mt) REVERT: C 42 LEU cc_start: 0.9451 (mt) cc_final: 0.9017 (mt) REVERT: C 55 ASP cc_start: 0.8164 (t70) cc_final: 0.7718 (t0) REVERT: C 82 TYR cc_start: 0.8818 (t80) cc_final: 0.8412 (t80) REVERT: D 13 LEU cc_start: 0.9005 (tt) cc_final: 0.8410 (tt) REVERT: D 15 LEU cc_start: 0.9401 (tp) cc_final: 0.9078 (tp) REVERT: D 17 ASN cc_start: 0.8976 (m-40) cc_final: 0.8478 (m110) REVERT: D 18 LEU cc_start: 0.9674 (mm) cc_final: 0.9463 (mm) REVERT: D 19 LEU cc_start: 0.9239 (mt) cc_final: 0.8773 (mt) REVERT: D 33 ASN cc_start: 0.9082 (m-40) cc_final: 0.8686 (m-40) REVERT: D 35 LEU cc_start: 0.9358 (mm) cc_final: 0.9074 (mm) REVERT: D 52 PHE cc_start: 0.9522 (t80) cc_final: 0.9138 (t80) REVERT: D 55 ASP cc_start: 0.8087 (t0) cc_final: 0.6821 (t0) REVERT: D 60 LYS cc_start: 0.8877 (pttt) cc_final: 0.7925 (pttt) REVERT: D 62 LEU cc_start: 0.9623 (tp) cc_final: 0.9288 (tp) REVERT: D 74 GLN cc_start: 0.8687 (mt0) cc_final: 0.7829 (mm-40) REVERT: D 84 ASN cc_start: 0.8338 (t0) cc_final: 0.8104 (t0) REVERT: D 89 ILE cc_start: 0.8162 (pt) cc_final: 0.7814 (mp) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1575 time to fit residues: 44.4370 Evaluate side-chains 178 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 27 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.8757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5966 Z= 0.341 Angle : 0.776 8.219 8100 Z= 0.413 Chirality : 0.045 0.194 835 Planarity : 0.004 0.034 1071 Dihedral : 5.500 35.297 784 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.49 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.28 (0.30), residues: 717 helix: 0.63 (0.25), residues: 402 sheet: 0.70 (0.80), residues: 44 loop : -0.43 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 156 HIS 0.012 0.003 HIS B 88 PHE 0.024 0.003 PHE D 25 TYR 0.027 0.002 TYR C 26 ARG 0.005 0.001 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8099 (m-80) cc_final: 0.7838 (m-80) REVERT: A 92 ASP cc_start: 0.6599 (t0) cc_final: 0.6017 (t0) REVERT: A 100 LEU cc_start: 0.9207 (mm) cc_final: 0.8970 (mm) REVERT: A 137 ASN cc_start: 0.7868 (t0) cc_final: 0.6870 (t0) REVERT: A 270 GLU cc_start: 0.8296 (tp30) cc_final: 0.7433 (tp30) REVERT: A 322 LEU cc_start: 0.8673 (tp) cc_final: 0.8370 (tp) REVERT: A 357 LEU cc_start: 0.9348 (tp) cc_final: 0.8919 (tp) REVERT: A 437 ASN cc_start: 0.8402 (p0) cc_final: 0.7282 (p0) REVERT: A 439 ASN cc_start: 0.9361 (t0) cc_final: 0.8762 (t0) REVERT: A 454 LEU cc_start: 0.9178 (tp) cc_final: 0.8867 (tp) REVERT: A 464 ASP cc_start: 0.7297 (p0) cc_final: 0.6969 (t0) REVERT: B 13 LEU cc_start: 0.9175 (tp) cc_final: 0.8658 (tp) REVERT: B 19 LEU cc_start: 0.7854 (mt) cc_final: 0.7621 (mt) REVERT: B 21 GLN cc_start: 0.6892 (tp40) cc_final: 0.6617 (tp-100) REVERT: B 33 ASN cc_start: 0.9186 (m-40) cc_final: 0.8923 (m-40) REVERT: B 89 ILE cc_start: 0.6958 (pt) cc_final: 0.6384 (pt) REVERT: C 2 THR cc_start: 0.7905 (m) cc_final: 0.7556 (m) REVERT: C 9 TYR cc_start: 0.8646 (m-10) cc_final: 0.8027 (m-10) REVERT: C 22 TRP cc_start: 0.8533 (m100) cc_final: 0.8321 (m100) REVERT: C 34 LEU cc_start: 0.9421 (tp) cc_final: 0.9145 (tp) REVERT: C 41 LEU cc_start: 0.9518 (mt) cc_final: 0.9254 (mt) REVERT: C 66 LEU cc_start: 0.8885 (pp) cc_final: 0.8630 (pp) REVERT: C 78 TYR cc_start: 0.7904 (t80) cc_final: 0.7561 (t80) REVERT: C 79 LYS cc_start: 0.8835 (ptpp) cc_final: 0.8471 (pttm) REVERT: D 13 LEU cc_start: 0.9425 (tt) cc_final: 0.8889 (tt) REVERT: D 15 LEU cc_start: 0.9298 (tp) cc_final: 0.8982 (tp) REVERT: D 17 ASN cc_start: 0.9099 (m-40) cc_final: 0.8534 (m110) REVERT: D 19 LEU cc_start: 0.9027 (mt) cc_final: 0.8755 (mt) REVERT: D 42 LEU cc_start: 0.9234 (mt) cc_final: 0.8935 (mt) REVERT: D 52 PHE cc_start: 0.9681 (t80) cc_final: 0.9391 (t80) REVERT: D 74 GLN cc_start: 0.8740 (mt0) cc_final: 0.7795 (mm-40) REVERT: D 78 TYR cc_start: 0.8430 (t80) cc_final: 0.8052 (t80) REVERT: D 82 TYR cc_start: 0.8865 (t80) cc_final: 0.8611 (t80) REVERT: D 84 ASN cc_start: 0.8405 (t0) cc_final: 0.8143 (t0) REVERT: D 89 ILE cc_start: 0.9309 (pt) cc_final: 0.8817 (mp) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1540 time to fit residues: 43.6779 Evaluate side-chains 168 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN C 88 HIS ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.8923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5966 Z= 0.178 Angle : 0.628 8.679 8100 Z= 0.330 Chirality : 0.042 0.201 835 Planarity : 0.003 0.035 1071 Dihedral : 4.901 37.001 784 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.21 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.59 (0.31), residues: 717 helix: 0.96 (0.26), residues: 402 sheet: 0.80 (0.78), residues: 42 loop : -0.42 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 75 HIS 0.005 0.001 HIS B 88 PHE 0.029 0.002 PHE C 52 TYR 0.026 0.002 TYR D 9 ARG 0.004 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8174 (m-80) cc_final: 0.7878 (m-80) REVERT: A 77 TRP cc_start: 0.7241 (m-90) cc_final: 0.6903 (m-90) REVERT: A 92 ASP cc_start: 0.6782 (t0) cc_final: 0.6136 (t0) REVERT: A 137 ASN cc_start: 0.7843 (t0) cc_final: 0.6863 (t0) REVERT: A 176 ASN cc_start: 0.8981 (t0) cc_final: 0.7661 (p0) REVERT: A 270 GLU cc_start: 0.8092 (tp30) cc_final: 0.7230 (tp30) REVERT: A 271 MET cc_start: 0.8363 (mmp) cc_final: 0.7831 (mmm) REVERT: A 322 LEU cc_start: 0.8670 (tp) cc_final: 0.8393 (tp) REVERT: A 437 ASN cc_start: 0.8509 (p0) cc_final: 0.7501 (p0) REVERT: A 439 ASN cc_start: 0.9335 (t0) cc_final: 0.8583 (t0) REVERT: B 21 GLN cc_start: 0.7095 (tp40) cc_final: 0.6671 (tp-100) REVERT: B 24 ASP cc_start: 0.7915 (t0) cc_final: 0.7146 (t0) REVERT: C 2 THR cc_start: 0.7872 (m) cc_final: 0.7584 (m) REVERT: C 9 TYR cc_start: 0.8598 (m-10) cc_final: 0.8344 (m-10) REVERT: C 32 ASN cc_start: 0.8640 (m110) cc_final: 0.8435 (m110) REVERT: C 41 LEU cc_start: 0.9556 (mt) cc_final: 0.9333 (mt) REVERT: C 78 TYR cc_start: 0.8062 (t80) cc_final: 0.7141 (t80) REVERT: C 82 TYR cc_start: 0.8966 (t80) cc_final: 0.8750 (t80) REVERT: D 7 GLN cc_start: 0.8565 (pt0) cc_final: 0.8251 (pt0) REVERT: D 13 LEU cc_start: 0.9403 (tt) cc_final: 0.8904 (tt) REVERT: D 17 ASN cc_start: 0.8936 (m-40) cc_final: 0.8264 (m110) REVERT: D 19 LEU cc_start: 0.9174 (mt) cc_final: 0.8791 (mt) REVERT: D 29 GLU cc_start: 0.8789 (mp0) cc_final: 0.8567 (mp0) REVERT: D 47 GLU cc_start: 0.8899 (pm20) cc_final: 0.8587 (pm20) REVERT: D 55 ASP cc_start: 0.7643 (t0) cc_final: 0.7111 (t0) REVERT: D 74 GLN cc_start: 0.8739 (mt0) cc_final: 0.7823 (mm-40) REVERT: D 78 TYR cc_start: 0.8396 (t80) cc_final: 0.8118 (t80) REVERT: D 82 TYR cc_start: 0.9016 (t80) cc_final: 0.8780 (t80) REVERT: D 84 ASN cc_start: 0.8424 (t0) cc_final: 0.8196 (t0) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1549 time to fit residues: 45.1031 Evaluate side-chains 165 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.9217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5966 Z= 0.161 Angle : 0.641 8.466 8100 Z= 0.332 Chirality : 0.042 0.216 835 Planarity : 0.004 0.035 1071 Dihedral : 4.612 29.753 784 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.21 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.52 (0.31), residues: 717 helix: 0.90 (0.26), residues: 402 sheet: 0.58 (0.72), residues: 44 loop : -0.41 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP B 75 HIS 0.003 0.001 HIS C 88 PHE 0.017 0.001 PHE D 77 TYR 0.025 0.001 TYR C 26 ARG 0.009 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8254 (m-80) cc_final: 0.8048 (m-10) REVERT: A 77 TRP cc_start: 0.6935 (m-90) cc_final: 0.6539 (m-90) REVERT: A 103 GLN cc_start: 0.8595 (mp10) cc_final: 0.8386 (mp10) REVERT: A 137 ASN cc_start: 0.7674 (t0) cc_final: 0.6796 (t0) REVERT: A 176 ASN cc_start: 0.9040 (t0) cc_final: 0.7846 (p0) REVERT: A 242 LYS cc_start: 0.8551 (mmpt) cc_final: 0.8298 (mtmt) REVERT: A 248 MET cc_start: 0.8774 (mpp) cc_final: 0.8484 (mpp) REVERT: A 261 LEU cc_start: 0.9301 (tp) cc_final: 0.9028 (tt) REVERT: A 270 GLU cc_start: 0.8089 (tp30) cc_final: 0.7085 (tp30) REVERT: A 271 MET cc_start: 0.8426 (mmp) cc_final: 0.7781 (mmm) REVERT: A 273 ASP cc_start: 0.8427 (m-30) cc_final: 0.8144 (m-30) REVERT: A 279 ASP cc_start: 0.8340 (p0) cc_final: 0.7451 (p0) REVERT: A 322 LEU cc_start: 0.8674 (tp) cc_final: 0.8402 (tp) REVERT: A 394 VAL cc_start: 0.7993 (t) cc_final: 0.7765 (t) REVERT: A 437 ASN cc_start: 0.8384 (p0) cc_final: 0.7317 (p0) REVERT: A 439 ASN cc_start: 0.9329 (t0) cc_final: 0.8568 (t0) REVERT: B 19 LEU cc_start: 0.7942 (mt) cc_final: 0.7650 (mt) REVERT: B 21 GLN cc_start: 0.6864 (tp40) cc_final: 0.6542 (tp-100) REVERT: C 2 THR cc_start: 0.7962 (m) cc_final: 0.7742 (m) REVERT: C 4 GLU cc_start: 0.8599 (mp0) cc_final: 0.8384 (mp0) REVERT: C 33 ASN cc_start: 0.9232 (m110) cc_final: 0.8967 (m-40) REVERT: C 41 LEU cc_start: 0.9548 (mt) cc_final: 0.9265 (mt) REVERT: C 78 TYR cc_start: 0.7905 (t80) cc_final: 0.7414 (t80) REVERT: C 82 TYR cc_start: 0.8865 (t80) cc_final: 0.8459 (t80) REVERT: D 9 TYR cc_start: 0.8471 (m-10) cc_final: 0.7975 (m-80) REVERT: D 13 LEU cc_start: 0.9277 (tt) cc_final: 0.8884 (tt) REVERT: D 17 ASN cc_start: 0.8857 (m-40) cc_final: 0.8140 (m110) REVERT: D 19 LEU cc_start: 0.9165 (mt) cc_final: 0.8837 (mt) REVERT: D 74 GLN cc_start: 0.8603 (mt0) cc_final: 0.7648 (mm-40) REVERT: D 78 TYR cc_start: 0.8383 (t80) cc_final: 0.7786 (t80) REVERT: D 82 TYR cc_start: 0.9045 (t80) cc_final: 0.8800 (t80) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1708 time to fit residues: 49.0508 Evaluate side-chains 172 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.0170 chunk 47 optimal weight: 9.9990 chunk 71 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN D 84 ASN D 88 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.9496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5966 Z= 0.164 Angle : 0.669 8.764 8100 Z= 0.343 Chirality : 0.043 0.224 835 Planarity : 0.004 0.035 1071 Dihedral : 4.528 20.971 784 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.49 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.35 (0.31), residues: 717 helix: 0.73 (0.26), residues: 401 sheet: 0.42 (0.72), residues: 44 loop : -0.41 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 75 HIS 0.004 0.001 HIS C 88 PHE 0.018 0.002 PHE C 77 TYR 0.016 0.001 TYR D 9 ARG 0.007 0.001 ARG A 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8740 (t0) cc_final: 0.8357 (t0) REVERT: A 19 PHE cc_start: 0.7917 (m-80) cc_final: 0.7660 (m-10) REVERT: A 103 GLN cc_start: 0.8484 (mp10) cc_final: 0.8256 (mp10) REVERT: A 137 ASN cc_start: 0.7700 (t0) cc_final: 0.6826 (t0) REVERT: A 242 LYS cc_start: 0.8540 (mmpt) cc_final: 0.8253 (mtmt) REVERT: A 270 GLU cc_start: 0.7916 (tp30) cc_final: 0.7608 (tp30) REVERT: A 279 ASP cc_start: 0.7673 (p0) cc_final: 0.7262 (p0) REVERT: A 322 LEU cc_start: 0.8578 (tp) cc_final: 0.8274 (tp) REVERT: A 437 ASN cc_start: 0.8300 (p0) cc_final: 0.7233 (p0) REVERT: A 439 ASN cc_start: 0.9290 (t0) cc_final: 0.8282 (t0) REVERT: B 19 LEU cc_start: 0.8066 (mt) cc_final: 0.7764 (mt) REVERT: B 21 GLN cc_start: 0.6928 (tp40) cc_final: 0.6669 (tp-100) REVERT: C 33 ASN cc_start: 0.9169 (m110) cc_final: 0.8966 (m-40) REVERT: C 41 LEU cc_start: 0.9504 (mt) cc_final: 0.9268 (mt) REVERT: C 89 ILE cc_start: 0.8459 (mp) cc_final: 0.8114 (mp) REVERT: D 13 LEU cc_start: 0.9210 (tt) cc_final: 0.8773 (tt) REVERT: D 17 ASN cc_start: 0.8719 (m-40) cc_final: 0.7881 (m110) REVERT: D 19 LEU cc_start: 0.9108 (mt) cc_final: 0.8735 (mt) REVERT: D 47 GLU cc_start: 0.8926 (pm20) cc_final: 0.8706 (pm20) REVERT: D 74 GLN cc_start: 0.8641 (mt0) cc_final: 0.7877 (mm-40) REVERT: D 78 TYR cc_start: 0.8661 (t80) cc_final: 0.8070 (t80) REVERT: D 89 ILE cc_start: 0.9209 (pt) cc_final: 0.8913 (mp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1612 time to fit residues: 44.4439 Evaluate side-chains 171 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 15 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 0.0020 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.092815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.073409 restraints weight = 25254.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075779 restraints weight = 14938.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077358 restraints weight = 9801.925| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.9718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5966 Z= 0.163 Angle : 0.661 8.534 8100 Z= 0.339 Chirality : 0.044 0.215 835 Planarity : 0.004 0.035 1071 Dihedral : 4.401 18.892 784 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.32 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.29 (0.31), residues: 717 helix: 0.63 (0.26), residues: 402 sheet: 0.95 (0.73), residues: 38 loop : -0.41 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 75 HIS 0.002 0.001 HIS C 88 PHE 0.016 0.002 PHE C 77 TYR 0.023 0.001 TYR C 26 ARG 0.007 0.001 ARG A 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1675.18 seconds wall clock time: 31 minutes 2.23 seconds (1862.23 seconds total)