Starting phenix.real_space_refine on Mon Jun 24 20:19:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/06_2024/8vzo_43684_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/06_2024/8vzo_43684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/06_2024/8vzo_43684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/06_2024/8vzo_43684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/06_2024/8vzo_43684_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzo_43684/06_2024/8vzo_43684_updated.pdb" } resolution = 2.49 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= 0.032 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 26 5.16 5 C 3152 2.51 5 N 765 2.21 5 O 853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 106": "NH1" <-> "NH2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "B GLU 1": "OE1" <-> "OE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 4796 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3235 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 15, 'TRANS': 400} Chain breaks: 1 Chain: "B" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1013 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "D" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 541 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.02, per 1000 atoms: 0.84 Number of scatterers: 4796 At special positions: 0 Unit cell: (74.7, 64.74, 106.24, 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 26 16.00 O 853 8.00 N 765 7.00 C 3152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 877.1 milliseconds 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 5 sheets defined 56.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 105 through 130 removed outlier: 3.531A pdb=" N LEU A 112 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN A 127 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N TYR A 128 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 130 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 removed outlier: 3.522A pdb=" N ASN A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 171 removed outlier: 3.815A pdb=" N LEU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 4.982A pdb=" N LEU A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 173 through 192 removed outlier: 4.459A pdb=" N LEU A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 216 removed outlier: 3.592A pdb=" N GLN A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 228 removed outlier: 3.557A pdb=" N ILE A 224 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 225 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 259 removed outlier: 3.516A pdb=" N CYS A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 294 removed outlier: 3.674A pdb=" N ALA A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 275 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 331 through 352 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 366 through 394 removed outlier: 3.716A pdb=" N LYS A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 416 Processing helix chain 'A' and resid 424 through 452 removed outlier: 4.184A pdb=" N LEU A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 458 through 487 removed outlier: 3.639A pdb=" N ASN A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 509 removed outlier: 3.561A pdb=" N ALA A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 518 No H-bonds generated for 'chain 'A' and resid 515 through 518' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'B' and resid 6 through 10 removed outlier: 3.544A pdb=" N LEU B 21 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 126 through 128 removed outlier: 6.404A pdb=" N ARG B 41 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.819A pdb=" N TYR B 121 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 86 through 91 removed outlier: 6.158A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 63 through 68 279 hydrogen bonds defined for protein. 747 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: 1.39 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 727 1.30 - 1.43: 1430 1.43 - 1.55: 2723 1.55 - 1.68: 2 1.68 - 1.81: 42 Bond restraints: 4924 Sorted by residual: bond pdb=" N PRO A 221 " pdb=" CD PRO A 221 " ideal model delta sigma weight residual 1.473 1.395 0.078 1.40e-02 5.10e+03 3.11e+01 bond pdb=" CA SER A 194 " pdb=" CB SER A 194 " ideal model delta sigma weight residual 1.535 1.457 0.077 1.51e-02 4.39e+03 2.63e+01 bond pdb=" C HIS A 198 " pdb=" O HIS A 198 " ideal model delta sigma weight residual 1.236 1.170 0.065 1.28e-02 6.10e+03 2.61e+01 bond pdb=" CA SER B 112 " pdb=" CB SER B 112 " ideal model delta sigma weight residual 1.528 1.461 0.066 1.35e-02 5.49e+03 2.41e+01 bond pdb=" N PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 1.473 1.404 0.069 1.40e-02 5.10e+03 2.41e+01 ... (remaining 4919 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.76: 138 105.76 - 112.96: 2360 112.96 - 120.16: 2308 120.16 - 127.36: 1842 127.36 - 134.55: 52 Bond angle restraints: 6700 Sorted by residual: angle pdb=" N ASP B 93 " pdb=" CA ASP B 93 " pdb=" C ASP B 93 " ideal model delta sigma weight residual 112.88 102.80 10.08 1.29e+00 6.01e-01 6.11e+01 angle pdb=" N LYS A 329 " pdb=" CA LYS A 329 " pdb=" C LYS A 329 " ideal model delta sigma weight residual 113.17 103.46 9.71 1.26e+00 6.30e-01 5.93e+01 angle pdb=" CA PHE D 99 " pdb=" CB PHE D 99 " pdb=" CG PHE D 99 " ideal model delta sigma weight residual 113.80 121.01 -7.21 1.00e+00 1.00e+00 5.20e+01 angle pdb=" N GLY B 18 " pdb=" CA GLY B 18 " pdb=" C GLY B 18 " ideal model delta sigma weight residual 115.36 106.09 9.27 1.33e+00 5.65e-01 4.85e+01 angle pdb=" CA TYR A 397 " pdb=" C TYR A 397 " pdb=" N LYS A 398 " ideal model delta sigma weight residual 117.48 126.79 -9.31 1.41e+00 5.03e-01 4.36e+01 ... (remaining 6695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 2544 17.52 - 35.03: 205 35.03 - 52.55: 56 52.55 - 70.07: 13 70.07 - 87.58: 7 Dihedral angle restraints: 2825 sinusoidal: 1053 harmonic: 1772 Sorted by residual: dihedral pdb=" CD ARG A 174 " pdb=" NE ARG A 174 " pdb=" CZ ARG A 174 " pdb=" NH1 ARG A 174 " ideal model delta sinusoidal sigma weight residual 0.00 -68.40 68.40 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " pdb=" CZ ARG B 90 " pdb=" NH1 ARG B 90 " ideal model delta sinusoidal sigma weight residual 0.00 57.15 -57.15 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CD ARG A 515 " pdb=" NE ARG A 515 " pdb=" CZ ARG A 515 " pdb=" NH1 ARG A 515 " ideal model delta sinusoidal sigma weight residual 0.00 44.54 -44.54 1 1.00e+01 1.00e-02 2.76e+01 ... (remaining 2822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 511 0.089 - 0.178: 187 0.178 - 0.267: 48 0.267 - 0.356: 13 0.356 - 0.445: 1 Chirality restraints: 760 Sorted by residual: chirality pdb=" CB VAL A 283 " pdb=" CA VAL A 283 " pdb=" CG1 VAL A 283 " pdb=" CG2 VAL A 283 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CB VAL B 8 " pdb=" CA VAL B 8 " pdb=" CG1 VAL B 8 " pdb=" CG2 VAL B 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ASP D 83 " pdb=" N ASP D 83 " pdb=" C ASP D 83 " pdb=" CB ASP D 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 757 not shown) Planarity restraints: 822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 174 " 1.013 9.50e-02 1.11e+02 4.54e-01 1.25e+02 pdb=" NE ARG A 174 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 174 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 174 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 174 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 90 " -0.924 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG B 90 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG B 90 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 90 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 90 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 515 " 0.778 9.50e-02 1.11e+02 3.49e-01 7.39e+01 pdb=" NE ARG A 515 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 515 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 515 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 515 " 0.025 2.00e-02 2.50e+03 ... (remaining 819 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1728 2.86 - 3.37: 4662 3.37 - 3.88: 8796 3.88 - 4.39: 10531 4.39 - 4.90: 16644 Nonbonded interactions: 42361 Sorted by model distance: nonbonded pdb=" O VAL A 414 " pdb=" OG1 THR A 418 " model vdw 2.347 2.440 nonbonded pdb=" OG SER B 20 " pdb=" O ASN B 87 " model vdw 2.381 2.440 nonbonded pdb=" N PHE B 30 " pdb=" O PHE B 30 " model vdw 2.407 2.496 nonbonded pdb=" N PHE B 107 " pdb=" O PHE B 107 " model vdw 2.414 2.496 nonbonded pdb=" O ALA A 306 " pdb=" OH TYR A 454 " model vdw 2.425 2.440 ... (remaining 42356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 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: 0.000 Extract box with map and model: 9.670 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.590 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.013 0.078 4924 Z= 0.864 Angle : 1.822 11.298 6700 Z= 1.331 Chirality : 0.100 0.445 760 Planarity : 0.030 0.454 822 Dihedral : 14.971 87.582 1694 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.67 % Allowed : 9.65 % Favored : 86.68 % Cbeta Deviations : 0.18 % 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: -2.36 (0.30), residues: 607 helix: -1.53 (0.24), residues: 345 sheet: -0.13 (0.59), residues: 77 loop : -1.90 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 122 HIS 0.014 0.002 HIS A 198 PHE 0.042 0.003 PHE D 99 TYR 0.036 0.003 TYR B 57 ARG 0.004 0.001 ARG A 515 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.485 Fit side-chains REVERT: A 101 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7927 (mm) REVERT: A 102 LYS cc_start: 0.7064 (tttt) cc_final: 0.6563 (tttm) REVERT: A 300 LYS cc_start: 0.7833 (tttp) cc_final: 0.7614 (tttp) REVERT: A 365 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 371 ARG cc_start: 0.7718 (mtt180) cc_final: 0.7472 (mtt180) REVERT: A 393 LYS cc_start: 0.7030 (ttpt) cc_final: 0.6370 (tttt) outliers start: 19 outliers final: 4 residues processed: 99 average time/residue: 1.0098 time to fit residues: 104.5863 Evaluate side-chains 61 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain D residue 97 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.0030 chunk 47 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 133 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 332 ASN A 368 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 520 ASN B 85 GLN D 38 GLN D 80 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4924 Z= 0.185 Angle : 0.566 7.588 6700 Z= 0.307 Chirality : 0.041 0.148 760 Planarity : 0.005 0.038 822 Dihedral : 5.446 45.399 673 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.93 % Allowed : 13.13 % Favored : 84.94 % 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: -0.11 (0.31), residues: 607 helix: 0.63 (0.26), residues: 341 sheet: 0.22 (0.58), residues: 76 loop : -1.38 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 228 HIS 0.002 0.001 HIS B 38 PHE 0.015 0.002 PHE A 495 TYR 0.022 0.001 TYR A 117 ARG 0.007 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.513 Fit side-chains REVERT: A 102 LYS cc_start: 0.7111 (tttt) cc_final: 0.6480 (tttm) REVERT: A 169 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: A 354 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8218 (tp) REVERT: A 365 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7064 (mm-30) REVERT: A 371 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7450 (mtt180) REVERT: A 393 LYS cc_start: 0.6982 (ttpt) cc_final: 0.6315 (tttm) outliers start: 10 outliers final: 3 residues processed: 63 average time/residue: 1.0182 time to fit residues: 67.3509 Evaluate side-chains 62 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 54 optimal weight: 0.0070 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN A 262 ASN A 361 HIS A 422 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4924 Z= 0.286 Angle : 0.581 7.150 6700 Z= 0.312 Chirality : 0.044 0.152 760 Planarity : 0.006 0.071 822 Dihedral : 5.339 46.876 666 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.70 % Allowed : 13.13 % Favored : 84.17 % 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: 0.54 (0.32), residues: 607 helix: 0.97 (0.26), residues: 347 sheet: 0.52 (0.59), residues: 75 loop : -0.76 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.003 0.001 HIS A 301 PHE 0.018 0.002 PHE A 495 TYR 0.024 0.002 TYR A 117 ARG 0.007 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.495 Fit side-chains REVERT: A 102 LYS cc_start: 0.7087 (tttt) cc_final: 0.6452 (tttm) REVERT: A 155 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7947 (mp) REVERT: A 354 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8294 (tp) REVERT: A 357 MET cc_start: 0.8029 (mmt) cc_final: 0.7664 (mmt) REVERT: A 365 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7291 (mm-30) REVERT: A 371 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7451 (mtt180) REVERT: A 393 LYS cc_start: 0.7257 (ttpt) cc_final: 0.6545 (tttm) outliers start: 14 outliers final: 6 residues processed: 60 average time/residue: 1.1446 time to fit residues: 71.8285 Evaluate side-chains 56 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4924 Z= 0.191 Angle : 0.508 6.792 6700 Z= 0.271 Chirality : 0.041 0.139 760 Planarity : 0.005 0.041 822 Dihedral : 5.020 42.413 666 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.32 % Allowed : 13.51 % Favored : 84.17 % 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: 1.11 (0.33), residues: 607 helix: 1.44 (0.26), residues: 345 sheet: 0.79 (0.61), residues: 75 loop : -0.54 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 122 HIS 0.002 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.022 0.001 TYR A 117 ARG 0.005 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.519 Fit side-chains REVERT: A 102 LYS cc_start: 0.7096 (tttt) cc_final: 0.6511 (ttpp) REVERT: A 357 MET cc_start: 0.8026 (mmt) cc_final: 0.7630 (mmt) REVERT: A 365 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 371 ARG cc_start: 0.7873 (mtt180) cc_final: 0.7458 (mtm180) REVERT: A 393 LYS cc_start: 0.7339 (ttpt) cc_final: 0.6593 (tttm) REVERT: A 420 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7448 (p0) REVERT: B 119 MET cc_start: 0.8449 (mtt) cc_final: 0.8236 (mtt) outliers start: 12 outliers final: 4 residues processed: 56 average time/residue: 0.9987 time to fit residues: 58.9412 Evaluate side-chains 54 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain B residue 54 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 34 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 132 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4924 Z= 0.234 Angle : 0.528 6.802 6700 Z= 0.282 Chirality : 0.042 0.150 760 Planarity : 0.005 0.055 822 Dihedral : 5.084 43.621 666 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.09 % Allowed : 12.93 % Favored : 83.98 % 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: 1.23 (0.33), residues: 607 helix: 1.43 (0.26), residues: 347 sheet: 0.96 (0.62), residues: 75 loop : -0.30 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 114 HIS 0.003 0.001 HIS A 361 PHE 0.019 0.002 PHE A 495 TYR 0.024 0.002 TYR A 117 ARG 0.005 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.521 Fit side-chains REVERT: A 102 LYS cc_start: 0.7117 (tttt) cc_final: 0.6547 (ttpp) REVERT: A 155 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8070 (mp) REVERT: A 253 PHE cc_start: 0.8339 (m-10) cc_final: 0.8017 (m-10) REVERT: A 354 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8230 (tp) REVERT: A 357 MET cc_start: 0.8046 (mmt) cc_final: 0.7591 (mmt) REVERT: A 371 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7484 (mtt180) REVERT: A 393 LYS cc_start: 0.7259 (ttpt) cc_final: 0.6584 (tttm) REVERT: A 420 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7463 (p0) REVERT: B 119 MET cc_start: 0.8421 (mtt) cc_final: 0.8190 (mtt) outliers start: 16 outliers final: 7 residues processed: 55 average time/residue: 1.0180 time to fit residues: 58.9903 Evaluate side-chains 57 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.0040 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4924 Z= 0.195 Angle : 0.501 6.730 6700 Z= 0.267 Chirality : 0.041 0.142 760 Planarity : 0.005 0.039 822 Dihedral : 4.916 41.257 666 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.51 % Allowed : 13.51 % Favored : 83.98 % 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: 1.46 (0.33), residues: 607 helix: 1.65 (0.27), residues: 345 sheet: 1.11 (0.62), residues: 75 loop : -0.28 (0.44), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 228 HIS 0.002 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.022 0.001 TYR A 117 ARG 0.004 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.517 Fit side-chains REVERT: A 102 LYS cc_start: 0.7116 (tttt) cc_final: 0.6535 (tttm) REVERT: A 253 PHE cc_start: 0.8305 (m-10) cc_final: 0.8017 (m-10) REVERT: A 354 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8203 (tp) REVERT: A 357 MET cc_start: 0.8036 (mmt) cc_final: 0.7565 (mmt) REVERT: A 371 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7416 (mtm180) REVERT: A 393 LYS cc_start: 0.7228 (ttpt) cc_final: 0.6579 (tttm) REVERT: A 420 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7495 (p0) REVERT: B 119 MET cc_start: 0.8405 (mtt) cc_final: 0.8145 (mtt) outliers start: 13 outliers final: 8 residues processed: 57 average time/residue: 1.0136 time to fit residues: 60.8798 Evaluate side-chains 59 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4924 Z= 0.219 Angle : 0.514 6.693 6700 Z= 0.274 Chirality : 0.041 0.148 760 Planarity : 0.005 0.047 822 Dihedral : 4.940 42.002 666 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.70 % Allowed : 13.51 % Favored : 83.78 % 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: 1.49 (0.33), residues: 607 helix: 1.60 (0.27), residues: 347 sheet: 1.25 (0.63), residues: 75 loop : -0.21 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 114 HIS 0.003 0.001 HIS A 361 PHE 0.019 0.002 PHE A 495 TYR 0.023 0.001 TYR A 117 ARG 0.004 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.523 Fit side-chains REVERT: A 102 LYS cc_start: 0.7132 (tttt) cc_final: 0.6563 (tttm) REVERT: A 155 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8049 (mp) REVERT: A 253 PHE cc_start: 0.8324 (m-10) cc_final: 0.8037 (m-10) REVERT: A 354 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8222 (tp) REVERT: A 357 MET cc_start: 0.8031 (mmt) cc_final: 0.7556 (mmt) REVERT: A 371 ARG cc_start: 0.7845 (mtt180) cc_final: 0.7481 (mtt180) REVERT: A 393 LYS cc_start: 0.7249 (ttpt) cc_final: 0.6601 (tttm) REVERT: A 420 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7507 (p0) REVERT: B 119 MET cc_start: 0.8380 (mtt) cc_final: 0.8140 (mtt) outliers start: 14 outliers final: 7 residues processed: 55 average time/residue: 1.0484 time to fit residues: 60.6805 Evaluate side-chains 58 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4924 Z= 0.210 Angle : 0.508 6.636 6700 Z= 0.270 Chirality : 0.041 0.145 760 Planarity : 0.005 0.045 822 Dihedral : 4.874 41.324 666 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.32 % Allowed : 13.90 % Favored : 83.78 % 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: 1.57 (0.33), residues: 607 helix: 1.69 (0.27), residues: 345 sheet: 1.33 (0.64), residues: 75 loop : -0.22 (0.44), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 114 HIS 0.003 0.001 HIS A 361 PHE 0.019 0.002 PHE A 495 TYR 0.022 0.001 TYR A 117 ARG 0.004 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.515 Fit side-chains REVERT: A 102 LYS cc_start: 0.7132 (tttt) cc_final: 0.6561 (tttm) REVERT: A 155 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8077 (mp) REVERT: A 253 PHE cc_start: 0.8315 (m-10) cc_final: 0.8012 (m-10) REVERT: A 354 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8212 (tp) REVERT: A 357 MET cc_start: 0.8031 (mmt) cc_final: 0.7550 (mmt) REVERT: A 371 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7507 (mtt180) REVERT: A 393 LYS cc_start: 0.7245 (ttpt) cc_final: 0.6584 (tttm) REVERT: A 420 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7494 (p0) REVERT: B 119 MET cc_start: 0.8366 (mtt) cc_final: 0.8059 (mtt) outliers start: 12 outliers final: 6 residues processed: 55 average time/residue: 1.0216 time to fit residues: 59.2268 Evaluate side-chains 57 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 55 optimal weight: 0.0030 chunk 47 optimal weight: 0.5980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4924 Z= 0.188 Angle : 0.495 6.519 6700 Z= 0.263 Chirality : 0.041 0.141 760 Planarity : 0.005 0.039 822 Dihedral : 4.768 40.112 666 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.51 % Allowed : 13.90 % Favored : 83.59 % 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: 1.67 (0.33), residues: 607 helix: 1.76 (0.27), residues: 345 sheet: 1.35 (0.64), residues: 75 loop : -0.16 (0.44), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 425 HIS 0.003 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.021 0.001 TYR A 117 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.478 Fit side-chains REVERT: A 102 LYS cc_start: 0.7136 (tttt) cc_final: 0.6535 (tttm) REVERT: A 155 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8105 (mp) REVERT: A 253 PHE cc_start: 0.8306 (m-10) cc_final: 0.8001 (m-10) REVERT: A 354 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8205 (tp) REVERT: A 357 MET cc_start: 0.8026 (mmt) cc_final: 0.7535 (mmt) REVERT: A 371 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7455 (mtm180) REVERT: A 393 LYS cc_start: 0.7240 (ttpt) cc_final: 0.6588 (tttm) REVERT: A 420 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7490 (p0) REVERT: B 119 MET cc_start: 0.8352 (mtt) cc_final: 0.8074 (mtt) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 1.0734 time to fit residues: 61.9686 Evaluate side-chains 59 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 0.0770 chunk 19 optimal weight: 0.8980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4924 Z= 0.204 Angle : 0.503 6.485 6700 Z= 0.268 Chirality : 0.041 0.144 760 Planarity : 0.005 0.042 822 Dihedral : 4.783 40.571 666 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.12 % Allowed : 14.48 % Favored : 83.40 % 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: 1.63 (0.33), residues: 607 helix: 1.72 (0.27), residues: 345 sheet: 1.36 (0.63), residues: 75 loop : -0.18 (0.44), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 425 HIS 0.003 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.022 0.001 TYR A 117 ARG 0.003 0.000 ARG A 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.559 Fit side-chains REVERT: A 102 LYS cc_start: 0.7135 (tttt) cc_final: 0.6568 (tttm) REVERT: A 155 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 253 PHE cc_start: 0.8316 (m-10) cc_final: 0.8010 (m-10) REVERT: A 354 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8210 (tp) REVERT: A 357 MET cc_start: 0.8037 (mmt) cc_final: 0.7538 (mmt) REVERT: A 371 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7546 (mtt180) REVERT: A 393 LYS cc_start: 0.7239 (ttpt) cc_final: 0.6588 (tttm) REVERT: A 420 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7497 (p0) REVERT: B 86 MET cc_start: 0.7165 (mtm) cc_final: 0.6905 (mtp) REVERT: B 119 MET cc_start: 0.8354 (mtt) cc_final: 0.8067 (mtt) outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 1.0533 time to fit residues: 59.7948 Evaluate side-chains 58 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.164136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119505 restraints weight = 4770.031| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.70 r_work: 0.3238 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4924 Z= 0.211 Angle : 0.508 6.546 6700 Z= 0.270 Chirality : 0.041 0.146 760 Planarity : 0.005 0.045 822 Dihedral : 4.804 40.910 666 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.12 % Allowed : 14.29 % Favored : 83.59 % 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: 1.58 (0.33), residues: 607 helix: 1.65 (0.27), residues: 347 sheet: 1.36 (0.63), residues: 75 loop : -0.15 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 114 HIS 0.003 0.001 HIS A 361 PHE 0.019 0.002 PHE A 495 TYR 0.023 0.001 TYR A 117 ARG 0.004 0.000 ARG A 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2078.71 seconds wall clock time: 37 minutes 57.16 seconds (2277.16 seconds total)