Starting phenix.real_space_refine on Tue Feb 13 18:50:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqu_34202/02_2024/8gqu_34202_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqu_34202/02_2024/8gqu_34202.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqu_34202/02_2024/8gqu_34202_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqu_34202/02_2024/8gqu_34202_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqu_34202/02_2024/8gqu_34202_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqu_34202/02_2024/8gqu_34202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqu_34202/02_2024/8gqu_34202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqu_34202/02_2024/8gqu_34202_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqu_34202/02_2024/8gqu_34202_trim_updated.pdb" } resolution = 3.5 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= 0.001 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 44 5.16 5 Cl 4 4.86 5 C 4846 2.51 5 N 1188 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 109": "OD1" <-> "OD2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 402": "OD1" <-> "OD2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B ASP 483": "OD1" <-> "OD2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 554": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7328 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3638 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 22, 'TRANS': 449} Chain: "B" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3638 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 22, 'TRANS': 449} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'GH6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'GH6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.34, per 1000 atoms: 0.59 Number of scatterers: 7328 At special positions: 0 Unit cell: (77.097, 116.06, 81.242, 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) Cl 4 17.00 S 44 16.00 O 1246 8.00 N 1188 7.00 C 4846 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 Atom "HETATM 7326 O17 GH6 B 901 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.4 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 72.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 90 through 125 Processing helix chain 'A' and resid 130 through 155 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.720A pdb=" N SER A 198 " --> pdb=" O CYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 225 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 237 through 252 removed outlier: 3.799A pdb=" N PHE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 272 through 295 Processing helix chain 'A' and resid 318 through 351 Proline residue: A 322 - end of helix Processing helix chain 'A' and resid 353 through 377 removed outlier: 8.159A pdb=" N LEU A 364 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 431 through 451 removed outlier: 4.541A pdb=" N TRP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 480 Processing helix chain 'A' and resid 496 through 512 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 531 through 548 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'B' and resid 90 through 125 Processing helix chain 'B' and resid 130 through 155 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.591A pdb=" N SER B 198 " --> pdb=" O CYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 225 removed outlier: 3.840A pdb=" N LEU B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.701A pdb=" N PHE B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 272 through 296 Processing helix chain 'B' and resid 318 through 351 Proline residue: B 322 - end of helix Processing helix chain 'B' and resid 353 through 377 removed outlier: 3.880A pdb=" N LYS B 362 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 364 " --> pdb=" O MET B 360 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU B 365 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 431 through 451 removed outlier: 4.440A pdb=" N TRP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 480 Processing helix chain 'B' and resid 496 through 512 Processing helix chain 'B' and resid 517 through 525 removed outlier: 3.510A pdb=" N PHE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 548 Processing helix chain 'B' and resid 552 through 559 484 hydrogen bonds defined for protein. 1269 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: 2.04 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2235 1.34 - 1.46: 1269 1.46 - 1.57: 3933 1.57 - 1.69: 1 1.69 - 1.81: 78 Bond restraints: 7516 Sorted by residual: bond pdb=" CG PRO B 315 " pdb=" CD PRO B 315 " ideal model delta sigma weight residual 1.503 1.434 0.069 3.40e-02 8.65e+02 4.11e+00 bond pdb=" CB PRO A 381 " pdb=" CG PRO A 381 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.77e+00 bond pdb=" CB PRO B 315 " pdb=" CG PRO B 315 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.61e+00 bond pdb=" C07 GH6 B 901 " pdb=" N08 GH6 B 901 " ideal model delta sigma weight residual 1.351 1.319 0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C09 GH6 A 901 " pdb=" N08 GH6 A 901 " ideal model delta sigma weight residual 1.352 1.320 0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 7511 not shown) Histogram of bond angle deviations from ideal: 96.09 - 103.68: 124 103.68 - 111.27: 3156 111.27 - 118.86: 2808 118.86 - 126.45: 4016 126.45 - 134.05: 132 Bond angle restraints: 10236 Sorted by residual: angle pdb=" N08 GH6 B 901 " pdb=" C09 GH6 B 901 " pdb=" N10 GH6 B 901 " ideal model delta sigma weight residual 90.93 119.80 -28.87 3.00e+00 1.11e-01 9.26e+01 angle pdb=" N08 GH6 A 901 " pdb=" C09 GH6 A 901 " pdb=" N10 GH6 A 901 " ideal model delta sigma weight residual 90.93 119.78 -28.85 3.00e+00 1.11e-01 9.25e+01 angle pdb=" C04 GH6 A 901 " pdb=" C09 GH6 A 901 " pdb=" N10 GH6 A 901 " ideal model delta sigma weight residual 141.87 120.31 21.56 3.00e+00 1.11e-01 5.16e+01 angle pdb=" C04 GH6 B 901 " pdb=" C09 GH6 B 901 " pdb=" N10 GH6 B 901 " ideal model delta sigma weight residual 141.87 120.33 21.54 3.00e+00 1.11e-01 5.16e+01 angle pdb=" CA PRO A 381 " pdb=" N PRO A 381 " pdb=" CD PRO A 381 " ideal model delta sigma weight residual 112.00 103.08 8.92 1.40e+00 5.10e-01 4.06e+01 ... (remaining 10231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3947 17.92 - 35.83: 307 35.83 - 53.75: 70 53.75 - 71.67: 16 71.67 - 89.58: 14 Dihedral angle restraints: 4354 sinusoidal: 1648 harmonic: 2706 Sorted by residual: dihedral pdb=" CA LEU B 548 " pdb=" C LEU B 548 " pdb=" N GLN B 549 " pdb=" CA GLN B 549 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE B 269 " pdb=" C PHE B 269 " pdb=" N PHE B 270 " pdb=" CA PHE B 270 " ideal model delta harmonic sigma weight residual 180.00 -163.76 -16.24 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA LEU A 548 " pdb=" C LEU A 548 " pdb=" N GLN A 549 " pdb=" CA GLN A 549 " ideal model delta harmonic sigma weight residual 180.00 -163.87 -16.13 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 994 0.054 - 0.109: 188 0.109 - 0.163: 17 0.163 - 0.218: 0 0.218 - 0.272: 1 Chirality restraints: 1200 Sorted by residual: chirality pdb=" CA ASP B 109 " pdb=" N ASP B 109 " pdb=" C ASP B 109 " pdb=" CB ASP B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA PRO A 381 " pdb=" N PRO A 381 " pdb=" C PRO A 381 " pdb=" CB PRO A 381 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CB ILE A 539 " pdb=" CA ILE A 539 " pdb=" CG1 ILE A 539 " pdb=" CG2 ILE A 539 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 1197 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 380 " 0.053 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO A 381 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 314 " -0.050 5.00e-02 4.00e+02 7.19e-02 8.28e+00 pdb=" N PRO B 315 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 314 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 315 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " -0.026 5.00e-02 4.00e+02 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 142 2.70 - 3.25: 7875 3.25 - 3.80: 12166 3.80 - 4.35: 14797 4.35 - 4.90: 24734 Nonbonded interactions: 59714 Sorted by model distance: nonbonded pdb=" CE LYS B 204 " pdb=" O17 GH6 B 901 " model vdw 2.151 3.440 nonbonded pdb=" OE1 GLU B 238 " pdb=" ND2 ASN B 274 " model vdw 2.222 2.520 nonbonded pdb=" O GLU B 166 " pdb=" OG1 THR B 169 " model vdw 2.264 2.440 nonbonded pdb=" O GLU A 166 " pdb=" OG1 THR A 169 " model vdw 2.270 2.440 nonbonded pdb=" OD1 ASN A 274 " pdb=" NH1 ARG A 277 " model vdw 2.271 2.520 ... (remaining 59709 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 3.770 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.350 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 7516 Z= 0.234 Angle : 0.837 28.870 10236 Z= 0.407 Chirality : 0.041 0.272 1200 Planarity : 0.005 0.075 1264 Dihedral : 14.945 89.584 2610 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 2.06 (0.28), residues: 940 helix: 2.13 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -0.68 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 444 HIS 0.011 0.002 HIS B 513 PHE 0.017 0.001 PHE A 279 TYR 0.015 0.001 TYR A 134 ARG 0.004 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6685 (tt0) REVERT: A 140 TYR cc_start: 0.7840 (t80) cc_final: 0.7495 (t80) REVERT: A 190 ILE cc_start: 0.8795 (mm) cc_final: 0.8430 (mm) REVERT: A 200 MET cc_start: 0.5763 (mmm) cc_final: 0.5297 (mmp) REVERT: A 270 PHE cc_start: 0.5169 (t80) cc_final: 0.4407 (t80) REVERT: A 309 ARG cc_start: 0.5749 (ttp-170) cc_final: 0.5145 (mtp-110) REVERT: A 377 LEU cc_start: 0.7974 (mt) cc_final: 0.7769 (tp) REVERT: B 190 ILE cc_start: 0.8730 (mm) cc_final: 0.8456 (mm) REVERT: B 490 SER cc_start: 0.6061 (t) cc_final: 0.5381 (p) REVERT: B 531 ILE cc_start: 0.8422 (tt) cc_final: 0.8216 (tt) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1894 time to fit residues: 69.1963 Evaluate side-chains 177 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.0170 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN B 127 ASN B 133 GLN B 296 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7516 Z= 0.194 Angle : 0.629 13.252 10236 Z= 0.312 Chirality : 0.040 0.149 1200 Planarity : 0.006 0.041 1264 Dihedral : 7.197 94.834 1014 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.83 % Allowed : 12.01 % Favored : 86.16 % 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: 1.83 (0.28), residues: 940 helix: 1.90 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.70 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 106 HIS 0.010 0.002 HIS B 486 PHE 0.012 0.001 PHE B 279 TYR 0.016 0.001 TYR A 134 ARG 0.007 0.001 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6981 (tm-30) cc_final: 0.6701 (tt0) REVERT: A 309 ARG cc_start: 0.5760 (ttp-170) cc_final: 0.5324 (mtm110) REVERT: B 490 SER cc_start: 0.5973 (t) cc_final: 0.5247 (p) REVERT: B 546 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7362 (mt0) REVERT: B 556 ILE cc_start: 0.8690 (mm) cc_final: 0.8203 (mt) outliers start: 14 outliers final: 7 residues processed: 193 average time/residue: 0.1741 time to fit residues: 46.1750 Evaluate side-chains 168 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 296 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7516 Z= 0.192 Angle : 0.573 9.001 10236 Z= 0.285 Chirality : 0.039 0.137 1200 Planarity : 0.005 0.038 1264 Dihedral : 6.751 97.514 1014 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.26 % Allowed : 14.23 % Favored : 82.51 % 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: 1.75 (0.28), residues: 940 helix: 1.84 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.71 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 106 HIS 0.003 0.001 HIS B 530 PHE 0.023 0.002 PHE A 280 TYR 0.009 0.001 TYR A 140 ARG 0.005 0.001 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 190 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.7000 (tm-30) cc_final: 0.6654 (tt0) REVERT: A 395 GLU cc_start: 0.6665 (tp30) cc_final: 0.6132 (tp30) REVERT: A 442 LYS cc_start: 0.8616 (mmtp) cc_final: 0.8370 (mmtm) REVERT: A 556 ILE cc_start: 0.8733 (mm) cc_final: 0.8278 (mt) REVERT: B 357 ARG cc_start: 0.5358 (tpt90) cc_final: 0.5032 (ptm160) REVERT: B 490 SER cc_start: 0.6163 (t) cc_final: 0.5430 (p) REVERT: B 546 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7514 (mt0) REVERT: B 556 ILE cc_start: 0.8721 (mm) cc_final: 0.8264 (mt) outliers start: 25 outliers final: 15 residues processed: 204 average time/residue: 0.1650 time to fit residues: 46.5047 Evaluate side-chains 177 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 542 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 0.0030 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7516 Z= 0.177 Angle : 0.557 10.238 10236 Z= 0.278 Chirality : 0.039 0.148 1200 Planarity : 0.005 0.039 1264 Dihedral : 6.695 100.772 1014 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.39 % Allowed : 16.32 % Favored : 80.29 % 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: 1.62 (0.28), residues: 940 helix: 1.72 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.70 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 106 HIS 0.002 0.001 HIS B 210 PHE 0.026 0.001 PHE B 279 TYR 0.007 0.001 TYR B 340 ARG 0.003 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.7099 (tm-30) cc_final: 0.6628 (tt0) REVERT: A 395 GLU cc_start: 0.6687 (tp30) cc_final: 0.6145 (tp30) REVERT: A 442 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8344 (mmtm) REVERT: B 279 PHE cc_start: 0.7820 (t80) cc_final: 0.7377 (t80) REVERT: B 490 SER cc_start: 0.6163 (t) cc_final: 0.5420 (p) outliers start: 26 outliers final: 15 residues processed: 180 average time/residue: 0.1655 time to fit residues: 41.3661 Evaluate side-chains 163 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 542 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7516 Z= 0.249 Angle : 0.650 15.834 10236 Z= 0.320 Chirality : 0.041 0.193 1200 Planarity : 0.005 0.040 1264 Dihedral : 6.674 87.773 1014 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.18 % Allowed : 17.23 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.37 (0.28), residues: 940 helix: 1.57 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.90 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 106 HIS 0.003 0.001 HIS B 530 PHE 0.019 0.002 PHE B 279 TYR 0.011 0.001 TYR B 230 ARG 0.003 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7987 (t80) REVERT: A 279 PHE cc_start: 0.7686 (t80) cc_final: 0.7393 (t80) REVERT: A 280 PHE cc_start: 0.7671 (t80) cc_final: 0.7319 (t80) REVERT: A 309 ARG cc_start: 0.5776 (ttp-170) cc_final: 0.4811 (mtp-110) REVERT: A 339 VAL cc_start: 0.8650 (t) cc_final: 0.8415 (m) REVERT: A 395 GLU cc_start: 0.6875 (tp30) cc_final: 0.6297 (tp30) REVERT: B 280 PHE cc_start: 0.7490 (t80) cc_final: 0.7237 (t80) REVERT: B 490 SER cc_start: 0.6181 (t) cc_final: 0.5533 (p) outliers start: 32 outliers final: 20 residues processed: 175 average time/residue: 0.1705 time to fit residues: 41.3537 Evaluate side-chains 162 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 542 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.2980 chunk 17 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7516 Z= 0.180 Angle : 0.612 16.470 10236 Z= 0.296 Chirality : 0.039 0.180 1200 Planarity : 0.005 0.041 1264 Dihedral : 6.432 81.253 1014 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.13 % Allowed : 18.54 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.59 (0.28), residues: 940 helix: 1.74 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -0.81 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 106 HIS 0.002 0.001 HIS B 210 PHE 0.027 0.001 PHE B 270 TYR 0.007 0.001 TYR A 275 ARG 0.007 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8068 (t80) REVERT: A 274 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6760 (t0) REVERT: A 395 GLU cc_start: 0.6799 (tp30) cc_final: 0.6575 (tp30) REVERT: B 101 MET cc_start: 0.7417 (tpt) cc_final: 0.7019 (tpp) REVERT: B 151 PHE cc_start: 0.7518 (t80) cc_final: 0.7286 (t80) REVERT: B 200 MET cc_start: 0.6138 (mmp) cc_final: 0.5858 (mmm) REVERT: B 280 PHE cc_start: 0.7441 (t80) cc_final: 0.7145 (t80) REVERT: B 490 SER cc_start: 0.6209 (t) cc_final: 0.5552 (p) outliers start: 24 outliers final: 14 residues processed: 168 average time/residue: 0.1552 time to fit residues: 36.6170 Evaluate side-chains 159 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 542 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 133 GLN B 296 ASN B 342 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 7516 Z= 0.215 Angle : 0.671 27.310 10236 Z= 0.313 Chirality : 0.040 0.195 1200 Planarity : 0.005 0.045 1264 Dihedral : 6.634 83.960 1014 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.13 % Allowed : 19.71 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.28), residues: 940 helix: 1.73 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -0.80 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 106 HIS 0.003 0.001 HIS B 210 PHE 0.022 0.002 PHE A 469 TYR 0.007 0.001 TYR B 340 ARG 0.010 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 205 GLU cc_start: 0.6264 (pm20) cc_final: 0.5821 (pt0) REVERT: A 208 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 239 MET cc_start: 0.6805 (mmp) cc_final: 0.6314 (mmp) REVERT: A 309 ARG cc_start: 0.5761 (ttp-170) cc_final: 0.4669 (mtp-110) REVERT: A 395 GLU cc_start: 0.6805 (tp30) cc_final: 0.6597 (tp30) REVERT: A 442 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8169 (mmtm) REVERT: B 151 PHE cc_start: 0.7567 (t80) cc_final: 0.7343 (t80) REVERT: B 280 PHE cc_start: 0.7420 (t80) cc_final: 0.7180 (t80) REVERT: B 490 SER cc_start: 0.6269 (t) cc_final: 0.5623 (p) outliers start: 24 outliers final: 18 residues processed: 161 average time/residue: 0.1668 time to fit residues: 37.3705 Evaluate side-chains 160 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 542 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.0020 chunk 17 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 0.0870 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 7516 Z= 0.174 Angle : 0.586 13.693 10236 Z= 0.287 Chirality : 0.039 0.182 1200 Planarity : 0.005 0.042 1264 Dihedral : 6.209 78.721 1014 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.00 % Allowed : 20.10 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.64 (0.29), residues: 940 helix: 1.78 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.79 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 106 HIS 0.002 0.001 HIS B 210 PHE 0.027 0.001 PHE B 270 TYR 0.009 0.001 TYR A 140 ARG 0.006 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.6870 (mmp) cc_final: 0.6432 (mmp) REVERT: A 333 PHE cc_start: 0.7740 (m-80) cc_final: 0.7481 (m-80) REVERT: A 395 GLU cc_start: 0.6838 (tp30) cc_final: 0.6294 (tp30) REVERT: A 442 LYS cc_start: 0.8642 (mmtp) cc_final: 0.8190 (mmtm) REVERT: B 151 PHE cc_start: 0.7627 (t80) cc_final: 0.7351 (t80) REVERT: B 208 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7393 (t80) REVERT: B 239 MET cc_start: 0.6614 (mmp) cc_final: 0.6374 (mmp) REVERT: B 280 PHE cc_start: 0.7353 (t80) cc_final: 0.7148 (t80) REVERT: B 490 SER cc_start: 0.6318 (t) cc_final: 0.5723 (p) outliers start: 23 outliers final: 16 residues processed: 163 average time/residue: 0.1690 time to fit residues: 37.9265 Evaluate side-chains 158 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 542 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 7516 Z= 0.223 Angle : 0.678 27.253 10236 Z= 0.317 Chirality : 0.041 0.195 1200 Planarity : 0.005 0.040 1264 Dihedral : 6.553 77.242 1014 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.87 % Allowed : 19.84 % Favored : 77.28 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.52 (0.29), residues: 940 helix: 1.70 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -0.88 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 106 HIS 0.002 0.001 HIS B 530 PHE 0.027 0.002 PHE A 469 TYR 0.009 0.001 TYR A 140 ARG 0.005 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.6873 (mmp) cc_final: 0.6572 (mmm) REVERT: A 270 PHE cc_start: 0.5867 (t80) cc_final: 0.5186 (t80) REVERT: A 333 PHE cc_start: 0.7747 (m-80) cc_final: 0.7484 (m-80) REVERT: A 395 GLU cc_start: 0.6828 (tp30) cc_final: 0.6291 (tp30) REVERT: A 442 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8191 (mmtm) REVERT: B 151 PHE cc_start: 0.7616 (t80) cc_final: 0.7330 (t80) REVERT: B 208 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7347 (t80) REVERT: B 280 PHE cc_start: 0.7375 (t80) cc_final: 0.7171 (t80) REVERT: B 490 SER cc_start: 0.6336 (t) cc_final: 0.5760 (p) outliers start: 22 outliers final: 17 residues processed: 160 average time/residue: 0.1449 time to fit residues: 33.5451 Evaluate side-chains 163 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 542 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 7516 Z= 0.259 Angle : 0.685 23.316 10236 Z= 0.329 Chirality : 0.042 0.208 1200 Planarity : 0.005 0.039 1264 Dihedral : 6.554 74.217 1014 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.35 % Allowed : 20.63 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.30 (0.29), residues: 940 helix: 1.58 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 480 HIS 0.003 0.001 HIS A 210 PHE 0.031 0.002 PHE B 270 TYR 0.010 0.001 TYR A 140 ARG 0.006 0.001 ARG B 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.6764 (mmp) cc_final: 0.6243 (mmm) REVERT: A 274 ASN cc_start: 0.7597 (t0) cc_final: 0.6886 (t0) REVERT: A 309 ARG cc_start: 0.5993 (ttp-170) cc_final: 0.4765 (mtp-110) REVERT: A 333 PHE cc_start: 0.7728 (m-80) cc_final: 0.7318 (m-80) REVERT: A 442 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8123 (mmtm) REVERT: A 445 MET cc_start: 0.8322 (mtm) cc_final: 0.8096 (mtp) REVERT: B 151 PHE cc_start: 0.7607 (t80) cc_final: 0.7385 (t80) REVERT: B 280 PHE cc_start: 0.7466 (t80) cc_final: 0.7220 (t80) REVERT: B 333 PHE cc_start: 0.7654 (m-80) cc_final: 0.7356 (m-80) REVERT: B 490 SER cc_start: 0.6345 (t) cc_final: 0.5838 (p) outliers start: 18 outliers final: 17 residues processed: 165 average time/residue: 0.1436 time to fit residues: 33.5244 Evaluate side-chains 157 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 542 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.0270 chunk 11 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** 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 = 0.3777 r_free = 0.3777 target = 0.152973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126663 restraints weight = 10924.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130150 restraints weight = 6661.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132346 restraints weight = 4947.696| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 7516 Z= 0.196 Angle : 0.624 18.381 10236 Z= 0.303 Chirality : 0.040 0.188 1200 Planarity : 0.005 0.040 1264 Dihedral : 6.272 74.744 1014 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.48 % Allowed : 21.28 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.47 (0.29), residues: 940 helix: 1.70 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.98 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 480 HIS 0.002 0.001 HIS B 210 PHE 0.030 0.001 PHE A 469 TYR 0.010 0.001 TYR A 140 ARG 0.004 0.000 ARG B 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.23 seconds wall clock time: 31 minutes 30.12 seconds (1890.12 seconds total)