Starting phenix.real_space_refine on Mon Mar 11 03:14:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/03_2024/8etm_28594_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/03_2024/8etm_28594.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/03_2024/8etm_28594_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/03_2024/8etm_28594_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/03_2024/8etm_28594_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/03_2024/8etm_28594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/03_2024/8etm_28594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/03_2024/8etm_28594_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/03_2024/8etm_28594_updated.pdb" } resolution = 3.2 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= 0.008 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: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 4524 2.51 5 N 1138 2.21 5 O 1090 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" 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: 6800 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'WTT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'WTT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.92, per 1000 atoms: 0.58 Number of scatterers: 6800 At special positions: 0 Unit cell: (112.88, 98.77, 83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 F 6 9.00 O 1090 8.00 N 1138 7.00 C 4524 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.2 seconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 0 sheets defined 70.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 88 through 111 removed outlier: 5.575A pdb=" N ARG A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 132 through 156 removed outlier: 4.316A pdb=" N ASN A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 191 through 227 removed outlier: 3.612A pdb=" N SER A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 275 through 305 removed outlier: 4.439A pdb=" N VAL A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 316 through 342 removed outlier: 3.885A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 371 through 374 No H-bonds generated for 'chain 'A' and resid 371 through 374' Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 429 through 447 removed outlier: 4.435A pdb=" N ILE A 438 " --> pdb=" O MET A 434 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 450 through 462 Processing helix chain 'A' and resid 466 through 477 removed outlier: 3.797A pdb=" N LEU A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 111 removed outlier: 5.575A pdb=" N ARG B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 132 through 156 removed outlier: 4.315A pdb=" N ASN B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 184 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 191 through 227 removed outlier: 3.612A pdb=" N SER B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 275 through 305 removed outlier: 4.440A pdb=" N VAL B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 316 through 342 removed outlier: 3.885A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 371 through 374 No H-bonds generated for 'chain 'B' and resid 371 through 374' Processing helix chain 'B' and resid 379 through 389 Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 400 through 419 Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 429 through 447 removed outlier: 4.434A pdb=" N ILE B 438 " --> pdb=" O MET B 434 " (cutoff:3.500A) Proline residue: B 439 - end of helix Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 466 through 477 removed outlier: 3.798A pdb=" N LEU B 470 " --> pdb=" O PRO B 466 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1140 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: 1.61 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1938 1.33 - 1.45: 1357 1.45 - 1.57: 3659 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 7022 Sorted by residual: bond pdb=" C14 WTT A 501 " pdb=" N1 WTT A 501 " ideal model delta sigma weight residual 1.476 1.331 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" C14 WTT B 501 " pdb=" N1 WTT B 501 " ideal model delta sigma weight residual 1.476 1.331 0.145 2.00e-02 2.50e+03 5.22e+01 bond pdb=" C10 WTT B 501 " pdb=" C9 WTT B 501 " ideal model delta sigma weight residual 1.561 1.475 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C10 WTT A 501 " pdb=" C9 WTT A 501 " ideal model delta sigma weight residual 1.561 1.475 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C20 WTT B 501 " pdb=" O1 WTT B 501 " ideal model delta sigma weight residual 1.412 1.333 0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 7017 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.32: 190 106.32 - 113.24: 3760 113.24 - 120.16: 2765 120.16 - 127.09: 2721 127.09 - 134.01: 126 Bond angle restraints: 9562 Sorted by residual: angle pdb=" N GLY A 464 " pdb=" CA GLY A 464 " pdb=" C GLY A 464 " ideal model delta sigma weight residual 113.18 121.08 -7.90 2.37e+00 1.78e-01 1.11e+01 angle pdb=" N GLY B 464 " pdb=" CA GLY B 464 " pdb=" C GLY B 464 " ideal model delta sigma weight residual 113.18 121.05 -7.87 2.37e+00 1.78e-01 1.10e+01 angle pdb=" C PHE B 342 " pdb=" N HIS B 343 " pdb=" CA HIS B 343 " ideal model delta sigma weight residual 122.42 116.69 5.73 1.77e+00 3.19e-01 1.05e+01 angle pdb=" C PHE A 342 " pdb=" N HIS A 343 " pdb=" CA HIS A 343 " ideal model delta sigma weight residual 122.42 116.70 5.72 1.77e+00 3.19e-01 1.04e+01 angle pdb=" C ILE B 379 " pdb=" CA ILE B 379 " pdb=" CB ILE B 379 " ideal model delta sigma weight residual 113.70 110.75 2.95 9.50e-01 1.11e+00 9.63e+00 ... (remaining 9557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 3795 23.98 - 47.96: 213 47.96 - 71.94: 20 71.94 - 95.92: 9 95.92 - 119.90: 1 Dihedral angle restraints: 4038 sinusoidal: 1626 harmonic: 2412 Sorted by residual: dihedral pdb=" CA ILE B 463 " pdb=" C ILE B 463 " pdb=" N GLY B 464 " pdb=" CA GLY B 464 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ILE A 463 " pdb=" C ILE A 463 " pdb=" N GLY A 464 " pdb=" CA GLY A 464 " ideal model delta harmonic sigma weight residual 180.00 156.82 23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLY A 87 " pdb=" C GLY A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 4035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.025: 1031 1.025 - 2.051: 0 2.051 - 3.076: 0 3.076 - 4.101: 0 4.101 - 5.127: 1 Chirality restraints: 1032 Sorted by residual: chirality pdb=" C5 WTT B 501 " pdb=" C28 WTT B 501 " pdb=" C4 WTT B 501 " pdb=" C6 WTT B 501 " both_signs ideal model delta sigma weight residual False -2.74 2.38 -5.13 2.00e-01 2.50e+01 6.57e+02 chirality pdb=" C5 WTT A 501 " pdb=" C28 WTT A 501 " pdb=" C4 WTT A 501 " pdb=" C6 WTT A 501 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C2 WTT A 501 " pdb=" C1 WTT A 501 " pdb=" C29 WTT A 501 " pdb=" C3 WTT A 501 " both_signs ideal model delta sigma weight residual False 2.73 2.58 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1029 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 WTT B 501 " -0.090 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C14 WTT B 501 " 0.082 2.00e-02 2.50e+03 pdb=" C15 WTT B 501 " -0.350 2.00e-02 2.50e+03 pdb=" N1 WTT B 501 " 0.537 2.00e-02 2.50e+03 pdb=" O2 WTT B 501 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WTT B 501 " -0.114 2.00e-02 2.50e+03 1.65e-01 7.45e+02 pdb=" C10 WTT B 501 " 0.025 2.00e-02 2.50e+03 pdb=" C11 WTT B 501 " -0.073 2.00e-02 2.50e+03 pdb=" C12 WTT B 501 " -0.171 2.00e-02 2.50e+03 pdb=" C13 WTT B 501 " -0.158 2.00e-02 2.50e+03 pdb=" C14 WTT B 501 " 0.419 2.00e-02 2.50e+03 pdb=" C23 WTT B 501 " -0.072 2.00e-02 2.50e+03 pdb=" C24 WTT B 501 " 0.013 2.00e-02 2.50e+03 pdb=" C25 WTT B 501 " 0.058 2.00e-02 2.50e+03 pdb=" C9 WTT B 501 " 0.175 2.00e-02 2.50e+03 pdb=" N2 WTT B 501 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 WTT A 501 " -0.161 2.00e-02 2.50e+03 1.86e-01 4.35e+02 pdb=" C14 WTT A 501 " 0.062 2.00e-02 2.50e+03 pdb=" C15 WTT A 501 " -0.223 2.00e-02 2.50e+03 pdb=" N1 WTT A 501 " 0.307 2.00e-02 2.50e+03 pdb=" O2 WTT A 501 " 0.016 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1497 2.76 - 3.30: 7110 3.30 - 3.83: 11454 3.83 - 4.37: 12928 4.37 - 4.90: 22338 Nonbonded interactions: 55327 Sorted by model distance: nonbonded pdb=" OE1 GLU A 351 " pdb=" NH2 ARG A 358 " model vdw 2.226 2.520 nonbonded pdb=" OE1 GLU B 351 " pdb=" NH2 ARG B 358 " model vdw 2.226 2.520 nonbonded pdb=" O TYR B 372 " pdb=" ND2 ASN B 376 " model vdw 2.249 2.520 nonbonded pdb=" O TYR A 372 " pdb=" ND2 ASN A 376 " model vdw 2.249 2.520 nonbonded pdb=" ND2 ASN B 378 " pdb=" O2 WTT B 501 " model vdw 2.252 2.520 ... (remaining 55322 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 'A' selection = chain 'B' } 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: 1.210 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: 3.870 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.370 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.009 0.145 7022 Z= 0.624 Angle : 0.845 8.373 9562 Z= 0.423 Chirality : 0.166 5.127 1032 Planarity : 0.013 0.302 1170 Dihedral : 15.266 119.900 2474 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % 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: -3.61 (0.24), residues: 804 helix: -1.46 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -4.91 (0.29), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 377 HIS 0.005 0.001 HIS B 474 PHE 0.017 0.002 PHE B 277 TYR 0.010 0.001 TYR A 417 ARG 0.002 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.803 Fit side-chains REVERT: A 131 TRP cc_start: 0.5126 (m-90) cc_final: 0.4065 (m100) REVERT: A 389 PHE cc_start: 0.7433 (t80) cc_final: 0.7165 (t80) REVERT: B 150 VAL cc_start: 0.7466 (t) cc_final: 0.7204 (t) REVERT: B 396 ARG cc_start: 0.3631 (ttm170) cc_final: 0.3219 (ttm170) REVERT: B 452 TYR cc_start: 0.7256 (m-80) cc_final: 0.6592 (m-80) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2574 time to fit residues: 47.5791 Evaluate side-chains 105 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 201 HIS A 292 GLN A 306 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 201 HIS B 292 GLN B 306 ASN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7022 Z= 0.223 Angle : 0.754 13.693 9562 Z= 0.336 Chirality : 0.041 0.138 1032 Planarity : 0.004 0.033 1170 Dihedral : 9.357 96.278 930 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.10 % Allowed : 12.89 % Favored : 85.01 % 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: -0.93 (0.30), residues: 804 helix: 0.43 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.84 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 377 HIS 0.003 0.001 HIS B 474 PHE 0.019 0.002 PHE B 389 TYR 0.012 0.001 TYR B 372 ARG 0.006 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 0.737 Fit side-chains REVERT: A 131 TRP cc_start: 0.5370 (m-90) cc_final: 0.4123 (m100) REVERT: A 199 MET cc_start: 0.7919 (tpp) cc_final: 0.7324 (tpt) REVERT: A 359 GLU cc_start: 0.7586 (tt0) cc_final: 0.7373 (tt0) REVERT: A 389 PHE cc_start: 0.7901 (t80) cc_final: 0.7620 (t80) REVERT: A 396 ARG cc_start: 0.3613 (ttm170) cc_final: 0.2981 (ttm170) REVERT: B 150 VAL cc_start: 0.7272 (t) cc_final: 0.7060 (t) REVERT: B 389 PHE cc_start: 0.7830 (t80) cc_final: 0.7455 (t80) REVERT: B 396 ARG cc_start: 0.3900 (ttm170) cc_final: 0.3464 (ttm170) REVERT: B 402 MET cc_start: 0.7696 (tmm) cc_final: 0.7456 (tmm) REVERT: B 442 TRP cc_start: 0.7311 (t60) cc_final: 0.7064 (t60) REVERT: B 452 TYR cc_start: 0.7389 (m-80) cc_final: 0.6720 (m-80) outliers start: 15 outliers final: 12 residues processed: 136 average time/residue: 0.2144 time to fit residues: 37.5699 Evaluate side-chains 113 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 337 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 0.0030 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN A 474 HIS B 107 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7022 Z= 0.221 Angle : 0.688 14.023 9562 Z= 0.316 Chirality : 0.042 0.229 1032 Planarity : 0.004 0.036 1170 Dihedral : 9.219 97.603 930 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.10 % Allowed : 15.13 % Favored : 82.77 % 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: -0.20 (0.31), residues: 804 helix: 1.01 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.68 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 377 HIS 0.005 0.001 HIS B 474 PHE 0.016 0.002 PHE B 389 TYR 0.009 0.001 TYR A 339 ARG 0.005 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.655 Fit side-chains REVERT: A 131 TRP cc_start: 0.5653 (m-90) cc_final: 0.4277 (m100) REVERT: A 396 ARG cc_start: 0.4145 (ttm170) cc_final: 0.3587 (ttm170) REVERT: A 425 MET cc_start: 0.8602 (mtt) cc_final: 0.8387 (mtt) REVERT: A 452 TYR cc_start: 0.7389 (m-80) cc_final: 0.6728 (m-80) REVERT: A 463 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7145 (tt) REVERT: B 396 ARG cc_start: 0.4200 (ttm170) cc_final: 0.3857 (ttm170) REVERT: B 402 MET cc_start: 0.7756 (tmm) cc_final: 0.7553 (tmm) REVERT: B 442 TRP cc_start: 0.7339 (t60) cc_final: 0.7137 (t60) REVERT: B 452 TYR cc_start: 0.7444 (m-80) cc_final: 0.6780 (m-80) REVERT: B 463 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7258 (tt) outliers start: 15 outliers final: 12 residues processed: 127 average time/residue: 0.2074 time to fit residues: 33.9467 Evaluate side-chains 114 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7022 Z= 0.293 Angle : 0.726 12.526 9562 Z= 0.338 Chirality : 0.044 0.202 1032 Planarity : 0.005 0.040 1170 Dihedral : 9.321 104.357 930 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 2.66 % Allowed : 16.81 % Favored : 80.53 % 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: -0.04 (0.31), residues: 804 helix: 1.10 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -3.58 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 377 HIS 0.003 0.001 HIS A 201 PHE 0.015 0.002 PHE B 426 TYR 0.009 0.001 TYR B 339 ARG 0.004 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.817 Fit side-chains REVERT: A 250 ARG cc_start: 0.6069 (ttt90) cc_final: 0.5770 (tpt170) REVERT: A 275 LYS cc_start: 0.7733 (mppt) cc_final: 0.7280 (pttp) REVERT: A 290 GLN cc_start: 0.7841 (tm-30) cc_final: 0.7454 (tt0) REVERT: A 396 ARG cc_start: 0.4534 (ttm170) cc_final: 0.4066 (ttm170) REVERT: A 402 MET cc_start: 0.7603 (tmm) cc_final: 0.7359 (tmm) REVERT: A 425 MET cc_start: 0.8890 (mtt) cc_final: 0.8526 (mtt) REVERT: B 138 ILE cc_start: 0.7517 (mm) cc_final: 0.7308 (mt) REVERT: B 250 ARG cc_start: 0.6174 (ttt90) cc_final: 0.5951 (tpt170) REVERT: B 275 LYS cc_start: 0.7681 (mppt) cc_final: 0.7227 (pttp) REVERT: B 396 ARG cc_start: 0.4592 (ttm170) cc_final: 0.4380 (ttm170) REVERT: B 402 MET cc_start: 0.7878 (tmm) cc_final: 0.7656 (tmm) REVERT: B 434 MET cc_start: 0.7662 (tpt) cc_final: 0.7320 (tpt) outliers start: 19 outliers final: 15 residues processed: 148 average time/residue: 0.2163 time to fit residues: 41.4316 Evaluate side-chains 125 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 0.0070 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7022 Z= 0.154 Angle : 0.678 12.092 9562 Z= 0.304 Chirality : 0.039 0.193 1032 Planarity : 0.004 0.033 1170 Dihedral : 8.966 97.433 930 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.66 % Allowed : 18.63 % Favored : 78.71 % 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: 0.43 (0.32), residues: 804 helix: 1.50 (0.23), residues: 598 sheet: None (None), residues: 0 loop : -3.57 (0.37), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.002 0.000 HIS B 201 PHE 0.010 0.001 PHE A 277 TYR 0.008 0.001 TYR B 372 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.740 Fit side-chains REVERT: A 250 ARG cc_start: 0.6078 (ttt90) cc_final: 0.5834 (tpt170) REVERT: A 275 LYS cc_start: 0.7712 (mppt) cc_final: 0.7282 (pttp) REVERT: A 290 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7422 (tt0) REVERT: A 324 LEU cc_start: 0.7074 (mm) cc_final: 0.6852 (mp) REVERT: A 353 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.5887 (ppp) REVERT: A 396 ARG cc_start: 0.4462 (ttm170) cc_final: 0.4087 (ttm170) REVERT: A 402 MET cc_start: 0.7796 (tmm) cc_final: 0.7555 (tmm) REVERT: B 138 ILE cc_start: 0.7576 (mm) cc_final: 0.7370 (mt) REVERT: B 250 ARG cc_start: 0.6097 (ttt90) cc_final: 0.5874 (tpt170) REVERT: B 275 LYS cc_start: 0.7662 (mppt) cc_final: 0.7235 (pttp) REVERT: B 324 LEU cc_start: 0.7028 (mm) cc_final: 0.6794 (mp) REVERT: B 353 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.6222 (ppp) REVERT: B 402 MET cc_start: 0.7830 (tmm) cc_final: 0.7606 (tmm) REVERT: B 416 GLU cc_start: 0.7047 (tp30) cc_final: 0.6778 (tp30) outliers start: 19 outliers final: 11 residues processed: 130 average time/residue: 0.2175 time to fit residues: 36.2481 Evaluate side-chains 123 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 386 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7022 Z= 0.405 Angle : 0.805 12.193 9562 Z= 0.370 Chirality : 0.045 0.241 1032 Planarity : 0.005 0.035 1170 Dihedral : 9.611 111.562 930 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 3.36 % Allowed : 19.47 % Favored : 77.17 % 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: 0.03 (0.31), residues: 804 helix: 1.11 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.55 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 377 HIS 0.004 0.001 HIS B 201 PHE 0.017 0.002 PHE B 426 TYR 0.015 0.002 TYR B 339 ARG 0.005 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.686 Fit side-chains REVERT: A 250 ARG cc_start: 0.6503 (ttt90) cc_final: 0.6124 (tpt170) REVERT: A 275 LYS cc_start: 0.7867 (mppt) cc_final: 0.7342 (pttp) REVERT: A 324 LEU cc_start: 0.7206 (mm) cc_final: 0.6951 (mp) REVERT: A 353 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.6349 (ppp) REVERT: A 396 ARG cc_start: 0.4946 (ttm170) cc_final: 0.4642 (ttm170) REVERT: A 416 GLU cc_start: 0.7265 (tp30) cc_final: 0.7014 (tp30) REVERT: A 434 MET cc_start: 0.7796 (tpt) cc_final: 0.7416 (tpt) REVERT: B 250 ARG cc_start: 0.6566 (ttt90) cc_final: 0.6201 (tpt170) REVERT: B 275 LYS cc_start: 0.7847 (mppt) cc_final: 0.7299 (pttp) REVERT: B 324 LEU cc_start: 0.7125 (mm) cc_final: 0.6886 (mp) REVERT: B 353 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.6647 (ppp) REVERT: B 402 MET cc_start: 0.8074 (tmm) cc_final: 0.7851 (tmm) REVERT: B 416 GLU cc_start: 0.7363 (tp30) cc_final: 0.7088 (tp30) REVERT: B 434 MET cc_start: 0.7782 (tpt) cc_final: 0.7505 (tpt) outliers start: 24 outliers final: 19 residues processed: 140 average time/residue: 0.2151 time to fit residues: 38.5133 Evaluate side-chains 137 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 77 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 454 ASN B 292 GLN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7022 Z= 0.174 Angle : 0.698 11.812 9562 Z= 0.312 Chirality : 0.040 0.183 1032 Planarity : 0.004 0.036 1170 Dihedral : 8.916 97.220 930 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.82 % Allowed : 21.99 % Favored : 76.19 % 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: 0.37 (0.32), residues: 804 helix: 1.39 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -3.65 (0.36), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 377 HIS 0.002 0.000 HIS B 201 PHE 0.011 0.001 PHE A 277 TYR 0.009 0.001 TYR A 339 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 250 ARG cc_start: 0.6391 (ttt90) cc_final: 0.6084 (tpt170) REVERT: A 275 LYS cc_start: 0.7804 (mppt) cc_final: 0.7313 (pttp) REVERT: A 324 LEU cc_start: 0.7114 (mm) cc_final: 0.6892 (mp) REVERT: A 353 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.5841 (ppp) REVERT: A 416 GLU cc_start: 0.7067 (tp30) cc_final: 0.6827 (tp30) REVERT: A 434 MET cc_start: 0.7777 (tpt) cc_final: 0.7419 (tpt) REVERT: B 199 MET cc_start: 0.7231 (tpp) cc_final: 0.7022 (tpp) REVERT: B 250 ARG cc_start: 0.6385 (ttt90) cc_final: 0.6070 (tpt170) REVERT: B 324 LEU cc_start: 0.7069 (mm) cc_final: 0.6854 (mp) REVERT: B 353 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.6422 (ppp) REVERT: B 402 MET cc_start: 0.7915 (tmm) cc_final: 0.7689 (tmm) REVERT: B 416 GLU cc_start: 0.7157 (tp30) cc_final: 0.6869 (tp30) REVERT: B 434 MET cc_start: 0.7766 (tpt) cc_final: 0.7475 (tpt) outliers start: 13 outliers final: 10 residues processed: 135 average time/residue: 0.2616 time to fit residues: 44.9973 Evaluate side-chains 130 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 386 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7022 Z= 0.160 Angle : 0.673 11.647 9562 Z= 0.302 Chirality : 0.040 0.188 1032 Planarity : 0.004 0.033 1170 Dihedral : 8.853 99.702 930 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.38 % Allowed : 22.97 % Favored : 74.65 % 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: 0.63 (0.32), residues: 804 helix: 1.59 (0.23), residues: 608 sheet: None (None), residues: 0 loop : -3.56 (0.37), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 377 HIS 0.002 0.000 HIS A 201 PHE 0.021 0.001 PHE A 443 TYR 0.012 0.001 TYR B 339 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.703 Fit side-chains REVERT: A 250 ARG cc_start: 0.6421 (ttt90) cc_final: 0.6075 (tpt170) REVERT: A 275 LYS cc_start: 0.7756 (mppt) cc_final: 0.7299 (pttp) REVERT: A 324 LEU cc_start: 0.7091 (mm) cc_final: 0.6874 (mp) REVERT: A 353 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.5853 (ppp) REVERT: A 434 MET cc_start: 0.7850 (tpt) cc_final: 0.7459 (tpt) REVERT: B 250 ARG cc_start: 0.6372 (ttt90) cc_final: 0.6115 (tpt170) REVERT: B 324 LEU cc_start: 0.7069 (mm) cc_final: 0.6851 (mp) REVERT: B 353 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.6373 (ppp) REVERT: B 402 MET cc_start: 0.8081 (tmm) cc_final: 0.7496 (tmm) REVERT: B 416 GLU cc_start: 0.7150 (tp30) cc_final: 0.6873 (tp30) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 0.2215 time to fit residues: 35.7022 Evaluate side-chains 123 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 386 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 56 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7022 Z= 0.214 Angle : 0.711 10.874 9562 Z= 0.317 Chirality : 0.041 0.195 1032 Planarity : 0.004 0.035 1170 Dihedral : 8.861 101.845 930 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.66 % Allowed : 22.83 % Favored : 74.51 % 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: 0.56 (0.32), residues: 804 helix: 1.56 (0.23), residues: 606 sheet: None (None), residues: 0 loop : -3.59 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 377 HIS 0.002 0.001 HIS B 201 PHE 0.011 0.001 PHE A 338 TYR 0.011 0.001 TYR B 339 ARG 0.004 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.780 Fit side-chains REVERT: A 250 ARG cc_start: 0.6465 (ttt90) cc_final: 0.6131 (tpt170) REVERT: A 275 LYS cc_start: 0.7753 (mppt) cc_final: 0.7296 (pttp) REVERT: A 292 GLN cc_start: 0.7634 (mt0) cc_final: 0.7402 (mt0) REVERT: A 324 LEU cc_start: 0.7117 (mm) cc_final: 0.6889 (mp) REVERT: A 353 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.5966 (ppp) REVERT: A 416 GLU cc_start: 0.7110 (tp30) cc_final: 0.6863 (tp30) REVERT: A 434 MET cc_start: 0.7805 (tpt) cc_final: 0.7452 (tpt) REVERT: B 250 ARG cc_start: 0.6457 (ttt90) cc_final: 0.6186 (tpt170) REVERT: B 292 GLN cc_start: 0.7600 (mt0) cc_final: 0.7379 (mt0) REVERT: B 324 LEU cc_start: 0.7060 (mm) cc_final: 0.6830 (mp) REVERT: B 353 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.6389 (ppp) REVERT: B 402 MET cc_start: 0.8107 (tmm) cc_final: 0.7861 (tmm) REVERT: B 416 GLU cc_start: 0.7184 (tp30) cc_final: 0.6909 (tp30) REVERT: B 434 MET cc_start: 0.7781 (tpt) cc_final: 0.7412 (tpt) outliers start: 19 outliers final: 13 residues processed: 126 average time/residue: 0.2222 time to fit residues: 35.9559 Evaluate side-chains 125 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.7060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7022 Z= 0.268 Angle : 0.748 12.023 9562 Z= 0.338 Chirality : 0.042 0.207 1032 Planarity : 0.004 0.034 1170 Dihedral : 9.025 105.085 930 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.96 % Allowed : 24.09 % Favored : 73.95 % 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: 0.50 (0.32), residues: 804 helix: 1.46 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.40 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 377 HIS 0.003 0.001 HIS B 201 PHE 0.028 0.002 PHE A 443 TYR 0.012 0.001 TYR B 339 ARG 0.004 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.790 Fit side-chains REVERT: A 250 ARG cc_start: 0.6592 (ttt90) cc_final: 0.6280 (tpt170) REVERT: A 275 LYS cc_start: 0.7773 (mppt) cc_final: 0.7306 (pttp) REVERT: A 292 GLN cc_start: 0.7686 (mt0) cc_final: 0.7442 (mt0) REVERT: A 324 LEU cc_start: 0.7137 (mm) cc_final: 0.6932 (mp) REVERT: A 353 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.6173 (ppp) REVERT: A 416 GLU cc_start: 0.7175 (tp30) cc_final: 0.6918 (tp30) REVERT: A 434 MET cc_start: 0.7855 (tpt) cc_final: 0.7544 (tpt) REVERT: B 250 ARG cc_start: 0.6574 (ttt90) cc_final: 0.6250 (tpt170) REVERT: B 292 GLN cc_start: 0.7625 (mt0) cc_final: 0.7375 (mt0) REVERT: B 324 LEU cc_start: 0.7116 (mm) cc_final: 0.6888 (mp) REVERT: B 353 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.6559 (ppp) REVERT: B 402 MET cc_start: 0.8158 (tmm) cc_final: 0.7914 (tmm) REVERT: B 416 GLU cc_start: 0.7213 (tp30) cc_final: 0.6924 (tp30) REVERT: B 434 MET cc_start: 0.7850 (tpt) cc_final: 0.7612 (tpt) outliers start: 14 outliers final: 12 residues processed: 121 average time/residue: 0.2293 time to fit residues: 35.8645 Evaluate side-chains 124 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.154648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123198 restraints weight = 9337.808| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.17 r_work: 0.3347 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7022 Z= 0.175 Angle : 0.709 11.771 9562 Z= 0.319 Chirality : 0.040 0.190 1032 Planarity : 0.004 0.035 1170 Dihedral : 8.788 98.537 930 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.10 % Allowed : 24.23 % Favored : 73.67 % 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: 0.59 (0.32), residues: 804 helix: 1.56 (0.23), residues: 608 sheet: None (None), residues: 0 loop : -3.56 (0.35), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.002 0.000 HIS B 201 PHE 0.013 0.001 PHE A 143 TYR 0.011 0.001 TYR B 339 ARG 0.004 0.000 ARG A 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.84 seconds wall clock time: 31 minutes 17.05 seconds (1877.05 seconds total)