Starting phenix.real_space_refine on Sat Apr 6 05:53:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/04_2024/7xja_33223.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/04_2024/7xja_33223.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/04_2024/7xja_33223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/04_2024/7xja_33223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/04_2024/7xja_33223.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/04_2024/7xja_33223.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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4808 2.51 5 N 1184 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7276 Number of models: 1 Model: "" Number of chains: 2 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} Time building chain proxies: 4.41, per 1000 atoms: 0.61 Number of scatterers: 7276 At special positions: 0 Unit cell: (80.413, 113.573, 79.584, 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 44 16.00 O 1240 8.00 N 1184 7.00 C 4808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.2 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... Secondary structure from input PDB file: 49 helices and 3 sheets defined 81.5% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 89 through 126 Processing helix chain 'A' and resid 129 through 156 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 181 through 198 Processing helix chain 'A' and resid 204 through 225 Processing helix chain 'A' and resid 226 through 231 removed outlier: 6.910A pdb=" N ILE A 229 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.609A pdb=" N PHE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.614A pdb=" N SER A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 296 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 320 through 352 removed outlier: 3.514A pdb=" N GLN A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 364 through 378 removed outlier: 3.556A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.726A pdb=" N GLN A 385 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 430 through 450 removed outlier: 4.142A pdb=" N TRP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 481 Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.872A pdb=" N TYR A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.425A pdb=" N VAL A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 549 Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'B' and resid 90 through 126 removed outlier: 3.514A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 156 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 181 through 198 Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.854A pdb=" N LEU B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 7.085A pdb=" N ILE B 229 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 253 removed outlier: 3.647A pdb=" N PHE B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.716A pdb=" N VAL B 259 " --> pdb=" O PRO B 255 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 296 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 320 through 352 Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 364 through 378 removed outlier: 3.574A pdb=" N ALA B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.674A pdb=" N GLN B 385 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 430 through 450 removed outlier: 4.073A pdb=" N TRP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 481 Processing helix chain 'B' and resid 495 through 513 removed outlier: 3.866A pdb=" N TYR B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 Processing helix chain 'B' and resid 530 through 549 Processing helix chain 'B' and resid 551 through 560 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA3, first strand: chain 'B' and resid 485 through 487 569 hydrogen bonds defined for protein. 1635 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: 3.03 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2238 1.35 - 1.46: 1850 1.46 - 1.58: 3298 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 7460 Sorted by residual: bond pdb=" CA VAL A 175 " pdb=" CB VAL A 175 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.11e-02 8.12e+03 9.56e-01 bond pdb=" N PRO B 453 " pdb=" CA PRO B 453 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 9.45e-01 bond pdb=" N PRO A 453 " pdb=" CA PRO A 453 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 9.26e-01 bond pdb=" CA VAL B 175 " pdb=" CB VAL B 175 " ideal model delta sigma weight residual 1.530 1.540 -0.011 1.11e-02 8.12e+03 8.99e-01 bond pdb=" CB PRO A 381 " pdb=" CG PRO A 381 " ideal model delta sigma weight residual 1.492 1.447 0.045 5.00e-02 4.00e+02 8.13e-01 ... (remaining 7455 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.35: 186 105.35 - 112.55: 3893 112.55 - 119.74: 2364 119.74 - 126.93: 3615 126.93 - 134.13: 102 Bond angle restraints: 10160 Sorted by residual: angle pdb=" CB MET B 167 " pdb=" CG MET B 167 " pdb=" SD MET B 167 " ideal model delta sigma weight residual 112.70 103.98 8.72 3.00e+00 1.11e-01 8.44e+00 angle pdb=" CB MET A 167 " pdb=" CG MET A 167 " pdb=" SD MET A 167 " ideal model delta sigma weight residual 112.70 104.08 8.62 3.00e+00 1.11e-01 8.26e+00 angle pdb=" C TYR B 230 " pdb=" N GLU B 231 " pdb=" CA GLU B 231 " ideal model delta sigma weight residual 121.94 116.23 5.71 2.00e+00 2.50e-01 8.16e+00 angle pdb=" CB MET A 460 " pdb=" CG MET A 460 " pdb=" SD MET A 460 " ideal model delta sigma weight residual 112.70 120.99 -8.29 3.00e+00 1.11e-01 7.63e+00 angle pdb=" CB MET B 360 " pdb=" CG MET B 360 " pdb=" SD MET B 360 " ideal model delta sigma weight residual 112.70 120.21 -7.51 3.00e+00 1.11e-01 6.26e+00 ... (remaining 10155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 3975 16.10 - 32.21: 260 32.21 - 48.31: 70 48.31 - 64.41: 17 64.41 - 80.52: 20 Dihedral angle restraints: 4342 sinusoidal: 1636 harmonic: 2706 Sorted by residual: dihedral pdb=" CG ARG A 558 " pdb=" CD ARG A 558 " pdb=" NE ARG A 558 " pdb=" CZ ARG A 558 " ideal model delta sinusoidal sigma weight residual -180.00 -138.50 -41.50 2 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CG ARG B 558 " pdb=" CD ARG B 558 " pdb=" NE ARG B 558 " pdb=" CZ ARG B 558 " ideal model delta sinusoidal sigma weight residual -180.00 -138.57 -41.43 2 1.50e+01 4.44e-03 9.34e+00 dihedral pdb=" CG ARG A 350 " pdb=" CD ARG A 350 " pdb=" NE ARG A 350 " pdb=" CZ ARG A 350 " ideal model delta sinusoidal sigma weight residual -180.00 -138.90 -41.10 2 1.50e+01 4.44e-03 9.22e+00 ... (remaining 4339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 734 0.029 - 0.057: 286 0.057 - 0.086: 125 0.086 - 0.114: 44 0.114 - 0.143: 11 Chirality restraints: 1200 Sorted by residual: chirality pdb=" CA GLU B 231 " pdb=" N GLU B 231 " pdb=" C GLU B 231 " pdb=" CB GLU B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA PHE B 284 " pdb=" N PHE B 284 " pdb=" C PHE B 284 " pdb=" CB PHE B 284 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VAL B 454 " pdb=" N VAL B 454 " pdb=" C VAL B 454 " pdb=" CB VAL B 454 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1197 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 444 " -0.019 2.00e-02 2.50e+03 1.45e-02 5.28e+00 pdb=" CG TRP A 444 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 444 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 444 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 444 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 444 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 444 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 444 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 444 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 444 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 444 " 0.012 2.00e-02 2.50e+03 1.25e-02 3.89e+00 pdb=" CG TRP B 444 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 444 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 444 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 444 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 444 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 444 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 444 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 444 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 444 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 379 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO B 380 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " -0.022 5.00e-02 4.00e+02 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 271 2.73 - 3.27: 7852 3.27 - 3.81: 12578 3.81 - 4.36: 13994 4.36 - 4.90: 24526 Nonbonded interactions: 59221 Sorted by model distance: nonbonded pdb=" O GLU B 166 " pdb=" OG1 THR B 169 " model vdw 2.182 2.440 nonbonded pdb=" OE2 GLU A 320 " pdb=" OH TYR A 499 " model vdw 2.222 2.440 nonbonded pdb=" OE2 GLU B 320 " pdb=" OH TYR B 499 " model vdw 2.226 2.440 nonbonded pdb=" O GLU A 166 " pdb=" OG1 THR A 169 " model vdw 2.233 2.440 nonbonded pdb=" O ASP A 402 " pdb=" NH1 ARG A 471 " model vdw 2.284 2.520 ... (remaining 59216 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: 0.910 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: 3.720 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.510 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 0.003 0.045 7460 Z= 0.170 Angle : 0.596 8.715 10160 Z= 0.332 Chirality : 0.039 0.143 1200 Planarity : 0.004 0.040 1256 Dihedral : 13.731 80.517 2598 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: 1.81 (0.28), residues: 940 helix: 1.78 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -0.40 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 444 HIS 0.012 0.002 HIS B 210 PHE 0.021 0.001 PHE B 147 TYR 0.016 0.001 TYR A 140 ARG 0.011 0.001 ARG B 277 *********************** 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 279 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.7116 (tt) cc_final: 0.6626 (pt) REVERT: A 170 ILE cc_start: 0.9021 (mm) cc_final: 0.8773 (mm) REVERT: A 288 ILE cc_start: 0.7953 (mm) cc_final: 0.7742 (mt) REVERT: A 309 ARG cc_start: 0.6199 (ttp-170) cc_final: 0.5062 (mmt-90) REVERT: A 374 ILE cc_start: 0.7585 (tt) cc_final: 0.7118 (mt) REVERT: A 433 LEU cc_start: 0.7917 (tp) cc_final: 0.7463 (mt) REVERT: A 515 VAL cc_start: 0.8225 (t) cc_final: 0.7969 (t) REVERT: B 153 GLN cc_start: 0.7612 (tp40) cc_final: 0.7344 (tm-30) REVERT: B 309 ARG cc_start: 0.5313 (mtm180) cc_final: 0.4758 (mmt-90) REVERT: B 320 GLU cc_start: 0.6376 (mt-10) cc_final: 0.5887 (mt-10) REVERT: B 433 LEU cc_start: 0.8048 (tp) cc_final: 0.7664 (mt) REVERT: B 477 MET cc_start: 0.7560 (ttm) cc_final: 0.7334 (ttt) REVERT: B 540 LEU cc_start: 0.8499 (mt) cc_final: 0.8255 (mp) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1946 time to fit residues: 71.5301 Evaluate side-chains 179 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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: 0.0870 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 542 ASN A 546 GLN B 542 ASN B 546 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7460 Z= 0.220 Angle : 0.582 8.264 10160 Z= 0.300 Chirality : 0.042 0.192 1200 Planarity : 0.005 0.040 1256 Dihedral : 3.572 14.598 1002 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.13 % Allowed : 9.53 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.28), residues: 940 helix: 2.27 (0.19), residues: 698 sheet: None (None), residues: 0 loop : -0.25 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 444 HIS 0.006 0.002 HIS A 210 PHE 0.020 0.002 PHE A 185 TYR 0.015 0.002 TYR B 340 ARG 0.005 0.001 ARG B 343 *********************** 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 211 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 0.654 Fit side-chains REVERT: A 131 LEU cc_start: 0.7505 (tt) cc_final: 0.7011 (pt) REVERT: A 170 ILE cc_start: 0.9123 (mm) cc_final: 0.8906 (mm) REVERT: A 305 LEU cc_start: 0.7746 (tp) cc_final: 0.7534 (tp) REVERT: A 309 ARG cc_start: 0.6532 (ttp-170) cc_final: 0.5062 (mmt-90) REVERT: A 408 ARG cc_start: 0.4683 (mmp-170) cc_final: 0.4080 (tpp-160) REVERT: A 433 LEU cc_start: 0.7877 (tp) cc_final: 0.7631 (mt) REVERT: B 108 MET cc_start: 0.7646 (mtt) cc_final: 0.7310 (mtp) REVERT: B 222 PHE cc_start: 0.6854 (t80) cc_final: 0.5055 (m-80) REVERT: B 309 ARG cc_start: 0.5496 (mtm180) cc_final: 0.4860 (mmt-90) REVERT: B 320 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6247 (mt-10) REVERT: B 395 GLU cc_start: 0.7366 (tp30) cc_final: 0.7123 (mt-10) REVERT: B 408 ARG cc_start: 0.3835 (mmm160) cc_final: 0.3379 (tpp-160) REVERT: B 433 LEU cc_start: 0.8060 (tp) cc_final: 0.7687 (mt) REVERT: B 477 MET cc_start: 0.7610 (ttm) cc_final: 0.7326 (ttt) REVERT: B 483 ASP cc_start: 0.6722 (t70) cc_final: 0.6403 (t0) outliers start: 24 outliers final: 18 residues processed: 202 average time/residue: 0.1784 time to fit residues: 49.2072 Evaluate side-chains 184 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 555 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 158 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN B 425 ASN B 542 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7460 Z= 0.328 Angle : 0.660 8.460 10160 Z= 0.346 Chirality : 0.045 0.187 1200 Planarity : 0.006 0.071 1256 Dihedral : 3.681 13.062 1002 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.92 % Allowed : 10.97 % Favored : 85.12 % 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: 2.21 (0.28), residues: 940 helix: 2.13 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -0.60 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 444 HIS 0.006 0.002 HIS A 513 PHE 0.025 0.003 PHE B 208 TYR 0.028 0.003 TYR B 134 ARG 0.017 0.001 ARG A 290 *********************** 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 197 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 0.786 Fit side-chains REVERT: A 158 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6980 (mt0) REVERT: A 222 PHE cc_start: 0.7148 (t80) cc_final: 0.4963 (m-10) REVERT: A 264 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 284 PHE cc_start: 0.7322 (t80) cc_final: 0.7101 (t80) REVERT: A 309 ARG cc_start: 0.6730 (ttp-170) cc_final: 0.5127 (mmt-90) REVERT: A 372 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 408 ARG cc_start: 0.5172 (mmp-170) cc_final: 0.4621 (tpp-160) REVERT: A 460 MET cc_start: 0.7750 (mmm) cc_final: 0.7473 (tpp) REVERT: B 108 MET cc_start: 0.7915 (mtt) cc_final: 0.7626 (mtp) REVERT: B 222 PHE cc_start: 0.6769 (t80) cc_final: 0.4973 (m-80) REVERT: B 264 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6865 (mm-30) REVERT: B 309 ARG cc_start: 0.5544 (mtm180) cc_final: 0.4569 (mmt-90) REVERT: B 395 GLU cc_start: 0.7507 (tp30) cc_final: 0.7278 (mt-10) REVERT: B 408 ARG cc_start: 0.4185 (mmm160) cc_final: 0.3750 (tpp-160) REVERT: B 477 MET cc_start: 0.7808 (ttm) cc_final: 0.7319 (ttt) REVERT: B 483 ASP cc_start: 0.7010 (t70) cc_final: 0.6659 (t0) REVERT: B 557 ILE cc_start: 0.8059 (tp) cc_final: 0.7836 (tp) outliers start: 30 outliers final: 19 residues processed: 189 average time/residue: 0.2384 time to fit residues: 61.1439 Evaluate side-chains 173 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 555 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7460 Z= 0.188 Angle : 0.530 6.839 10160 Z= 0.273 Chirality : 0.041 0.145 1200 Planarity : 0.004 0.042 1256 Dihedral : 3.442 12.336 1002 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.61 % Allowed : 14.75 % Favored : 82.64 % 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: 2.48 (0.28), residues: 940 helix: 2.37 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -0.67 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 444 HIS 0.005 0.002 HIS A 513 PHE 0.021 0.002 PHE A 314 TYR 0.015 0.001 TYR A 492 ARG 0.009 0.001 ARG A 273 *********************** 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 186 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.6646 (ttp-170) cc_final: 0.4999 (mmt-90) REVERT: A 372 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8466 (tt) REVERT: A 408 ARG cc_start: 0.5136 (mmp-170) cc_final: 0.4629 (tpp-160) REVERT: B 108 MET cc_start: 0.7953 (mtt) cc_final: 0.7669 (mtp) REVERT: B 222 PHE cc_start: 0.6669 (t80) cc_final: 0.4936 (m-80) REVERT: B 264 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6979 (mm-30) REVERT: B 309 ARG cc_start: 0.5459 (mtm180) cc_final: 0.4450 (mmt-90) REVERT: B 348 VAL cc_start: 0.8529 (t) cc_final: 0.8059 (m) REVERT: B 395 GLU cc_start: 0.7455 (tp30) cc_final: 0.7234 (mt-10) REVERT: B 408 ARG cc_start: 0.4129 (mmm160) cc_final: 0.3558 (tpp-160) REVERT: B 477 MET cc_start: 0.7728 (ttm) cc_final: 0.7442 (ttt) REVERT: B 483 ASP cc_start: 0.6888 (t70) cc_final: 0.6144 (m-30) REVERT: B 557 ILE cc_start: 0.8055 (tp) cc_final: 0.7802 (tp) outliers start: 20 outliers final: 15 residues processed: 179 average time/residue: 0.1861 time to fit residues: 44.9979 Evaluate side-chains 170 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 431 VAL 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: 1.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7460 Z= 0.185 Angle : 0.521 6.645 10160 Z= 0.269 Chirality : 0.040 0.139 1200 Planarity : 0.004 0.042 1256 Dihedral : 3.347 11.778 1002 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.13 % Allowed : 14.10 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.28), residues: 940 helix: 2.57 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -0.72 (0.43), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 444 HIS 0.007 0.002 HIS A 210 PHE 0.026 0.002 PHE A 147 TYR 0.023 0.002 TYR B 134 ARG 0.006 0.000 ARG A 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 188 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.6680 (ttp-170) cc_final: 0.4974 (mmt-90) REVERT: A 372 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8510 (tt) REVERT: A 408 ARG cc_start: 0.5269 (mmp-170) cc_final: 0.4555 (tpp-160) REVERT: B 108 MET cc_start: 0.7939 (mtt) cc_final: 0.7684 (mtp) REVERT: B 222 PHE cc_start: 0.6337 (t80) cc_final: 0.5132 (m-10) REVERT: B 264 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7098 (mm-30) REVERT: B 309 ARG cc_start: 0.5571 (mtm180) cc_final: 0.4553 (mmt-90) REVERT: B 348 VAL cc_start: 0.8511 (t) cc_final: 0.8029 (m) REVERT: B 395 GLU cc_start: 0.7405 (tp30) cc_final: 0.7132 (mt-10) REVERT: B 408 ARG cc_start: 0.4143 (mmm160) cc_final: 0.3595 (tpp-160) REVERT: B 477 MET cc_start: 0.7750 (ttm) cc_final: 0.7450 (ttt) REVERT: B 483 ASP cc_start: 0.6947 (t70) cc_final: 0.6228 (m-30) REVERT: B 557 ILE cc_start: 0.8047 (tp) cc_final: 0.7790 (tp) outliers start: 24 outliers final: 17 residues processed: 183 average time/residue: 0.1951 time to fit residues: 48.8340 Evaluate side-chains 174 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7460 Z= 0.177 Angle : 0.525 8.294 10160 Z= 0.271 Chirality : 0.040 0.138 1200 Planarity : 0.004 0.041 1256 Dihedral : 3.329 11.566 1002 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.26 % Allowed : 15.14 % Favored : 81.59 % 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: 2.65 (0.28), residues: 940 helix: 2.58 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -0.74 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 444 HIS 0.005 0.002 HIS B 210 PHE 0.020 0.002 PHE A 279 TYR 0.013 0.001 TYR A 275 ARG 0.005 0.000 ARG A 343 *********************** 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 191 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.6882 (t80) cc_final: 0.5224 (m-10) REVERT: A 223 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7194 (mm) REVERT: A 309 ARG cc_start: 0.6656 (ttp-170) cc_final: 0.4956 (mmt-90) REVERT: A 372 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8552 (tt) REVERT: A 408 ARG cc_start: 0.5391 (mmp-170) cc_final: 0.4672 (tpp-160) REVERT: B 108 MET cc_start: 0.7918 (mtt) cc_final: 0.7695 (mtp) REVERT: B 222 PHE cc_start: 0.6267 (t80) cc_final: 0.5130 (m-10) REVERT: B 264 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7113 (mm-30) REVERT: B 309 ARG cc_start: 0.5547 (mtm180) cc_final: 0.4499 (mmt-90) REVERT: B 348 VAL cc_start: 0.8489 (t) cc_final: 0.8017 (m) REVERT: B 395 GLU cc_start: 0.7410 (tp30) cc_final: 0.7182 (mt-10) REVERT: B 408 ARG cc_start: 0.4103 (mmm160) cc_final: 0.3590 (tpp-160) REVERT: B 477 MET cc_start: 0.7728 (ttm) cc_final: 0.7439 (ttt) REVERT: B 483 ASP cc_start: 0.7014 (t70) cc_final: 0.6343 (m-30) REVERT: B 523 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7638 (mt-10) REVERT: B 557 ILE cc_start: 0.8058 (tp) cc_final: 0.7814 (tp) outliers start: 25 outliers final: 18 residues processed: 184 average time/residue: 0.1899 time to fit residues: 46.9149 Evaluate side-chains 177 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 0.0060 chunk 54 optimal weight: 1.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7460 Z= 0.196 Angle : 0.538 6.348 10160 Z= 0.279 Chirality : 0.041 0.203 1200 Planarity : 0.004 0.041 1256 Dihedral : 3.369 11.663 1002 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.79 % Allowed : 16.06 % Favored : 80.16 % 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: 2.62 (0.28), residues: 940 helix: 2.57 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -0.77 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 444 HIS 0.004 0.002 HIS B 210 PHE 0.020 0.002 PHE A 280 TYR 0.026 0.002 TYR B 134 ARG 0.004 0.000 ARG A 343 *********************** 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 186 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.6943 (t80) cc_final: 0.5282 (m-10) REVERT: A 223 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7232 (mm) REVERT: A 309 ARG cc_start: 0.6722 (ttp-170) cc_final: 0.5067 (mmt-90) REVERT: A 348 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.7932 (m) REVERT: A 372 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8601 (tt) REVERT: A 408 ARG cc_start: 0.5517 (mmp-170) cc_final: 0.4568 (tpp-160) REVERT: B 108 MET cc_start: 0.7958 (mtt) cc_final: 0.7734 (mtp) REVERT: B 222 PHE cc_start: 0.6606 (t80) cc_final: 0.4959 (m-80) REVERT: B 264 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7204 (mm-30) REVERT: B 309 ARG cc_start: 0.5663 (mtm180) cc_final: 0.4567 (mmt-90) REVERT: B 348 VAL cc_start: 0.8461 (t) cc_final: 0.8030 (m) REVERT: B 362 LYS cc_start: 0.7570 (mttt) cc_final: 0.7230 (mmtt) REVERT: B 395 GLU cc_start: 0.7452 (tp30) cc_final: 0.7225 (mt-10) REVERT: B 408 ARG cc_start: 0.4016 (mmm160) cc_final: 0.3518 (tpp-160) REVERT: B 477 MET cc_start: 0.7717 (ttm) cc_final: 0.7409 (ttt) REVERT: B 483 ASP cc_start: 0.7046 (t70) cc_final: 0.6418 (m-30) REVERT: B 557 ILE cc_start: 0.8090 (tp) cc_final: 0.7889 (tp) outliers start: 29 outliers final: 19 residues processed: 178 average time/residue: 0.1891 time to fit residues: 45.2646 Evaluate side-chains 175 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7460 Z= 0.186 Angle : 0.538 8.104 10160 Z= 0.276 Chirality : 0.041 0.232 1200 Planarity : 0.004 0.041 1256 Dihedral : 3.335 13.781 1002 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.66 % Allowed : 16.97 % Favored : 79.37 % 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: 2.54 (0.28), residues: 940 helix: 2.54 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.86 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 444 HIS 0.007 0.002 HIS A 513 PHE 0.021 0.002 PHE B 279 TYR 0.012 0.001 TYR A 275 ARG 0.004 0.000 ARG A 343 *********************** 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 191 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.6970 (t80) cc_final: 0.5318 (m-10) REVERT: A 223 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7282 (mm) REVERT: A 309 ARG cc_start: 0.6707 (ttp-170) cc_final: 0.5059 (mmt-90) REVERT: A 348 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.7955 (m) REVERT: A 372 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8599 (tt) REVERT: A 408 ARG cc_start: 0.5547 (mmp-170) cc_final: 0.4604 (tpp-160) REVERT: B 108 MET cc_start: 0.7943 (mtt) cc_final: 0.7724 (mtp) REVERT: B 222 PHE cc_start: 0.6731 (t80) cc_final: 0.5105 (m-10) REVERT: B 309 ARG cc_start: 0.5686 (mtm180) cc_final: 0.4551 (mmt-90) REVERT: B 348 VAL cc_start: 0.8471 (t) cc_final: 0.8053 (m) REVERT: B 362 LYS cc_start: 0.7598 (mttt) cc_final: 0.7272 (mmtt) REVERT: B 408 ARG cc_start: 0.4179 (mmm160) cc_final: 0.3656 (tpp-160) REVERT: B 477 MET cc_start: 0.7731 (ttm) cc_final: 0.7426 (ttt) REVERT: B 483 ASP cc_start: 0.7067 (t70) cc_final: 0.6470 (m-30) outliers start: 28 outliers final: 20 residues processed: 183 average time/residue: 0.1839 time to fit residues: 45.9431 Evaluate side-chains 183 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7460 Z= 0.217 Angle : 0.573 8.630 10160 Z= 0.294 Chirality : 0.043 0.343 1200 Planarity : 0.004 0.041 1256 Dihedral : 3.370 13.154 1002 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.18 % Allowed : 16.84 % Favored : 78.98 % 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: 2.48 (0.28), residues: 940 helix: 2.48 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -0.89 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 444 HIS 0.007 0.002 HIS B 210 PHE 0.030 0.002 PHE A 279 TYR 0.022 0.002 TYR B 134 ARG 0.007 0.001 ARG A 273 *********************** 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 195 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.6920 (t80) cc_final: 0.5289 (m-10) REVERT: A 223 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7306 (mm) REVERT: A 262 SER cc_start: 0.8507 (t) cc_final: 0.8212 (m) REVERT: A 309 ARG cc_start: 0.6529 (ttp-170) cc_final: 0.4955 (mmt-90) REVERT: A 348 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.7966 (m) REVERT: A 372 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8605 (tt) REVERT: A 408 ARG cc_start: 0.5588 (mmp-170) cc_final: 0.4618 (tpp-160) REVERT: B 108 MET cc_start: 0.7965 (mtt) cc_final: 0.7740 (mtp) REVERT: B 222 PHE cc_start: 0.6883 (t80) cc_final: 0.5233 (m-10) REVERT: B 309 ARG cc_start: 0.5644 (mtm180) cc_final: 0.4528 (mmt-90) REVERT: B 320 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6271 (mt-10) REVERT: B 348 VAL cc_start: 0.8494 (t) cc_final: 0.8087 (m) REVERT: B 362 LYS cc_start: 0.7610 (mttt) cc_final: 0.7301 (mmtt) REVERT: B 408 ARG cc_start: 0.4351 (mmm160) cc_final: 0.3776 (tpp-160) REVERT: B 477 MET cc_start: 0.7757 (ttm) cc_final: 0.7372 (ttt) REVERT: B 483 ASP cc_start: 0.6995 (t70) cc_final: 0.6470 (m-30) outliers start: 32 outliers final: 23 residues processed: 186 average time/residue: 0.1912 time to fit residues: 47.5653 Evaluate side-chains 188 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.0570 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7460 Z= 0.178 Angle : 0.563 11.167 10160 Z= 0.284 Chirality : 0.042 0.365 1200 Planarity : 0.004 0.052 1256 Dihedral : 3.317 12.974 1002 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.87 % Allowed : 18.02 % Favored : 79.11 % 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: 2.56 (0.28), residues: 940 helix: 2.56 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -0.89 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 444 HIS 0.005 0.002 HIS B 210 PHE 0.029 0.001 PHE A 279 TYR 0.011 0.001 TYR A 275 ARG 0.005 0.000 ARG B 350 ********************** 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 186 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.7834 (mmm) cc_final: 0.7615 (mmm) REVERT: A 222 PHE cc_start: 0.6975 (t80) cc_final: 0.5290 (m-10) REVERT: A 223 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7295 (mm) REVERT: A 262 SER cc_start: 0.8532 (t) cc_final: 0.8193 (m) REVERT: A 309 ARG cc_start: 0.6454 (ttp-170) cc_final: 0.4945 (mmt-90) REVERT: A 348 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.7938 (m) REVERT: A 362 LYS cc_start: 0.7396 (mttt) cc_final: 0.7089 (mmtt) REVERT: A 372 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8602 (tt) REVERT: B 108 MET cc_start: 0.7941 (mtt) cc_final: 0.7710 (mtp) REVERT: B 222 PHE cc_start: 0.6744 (t80) cc_final: 0.5108 (m-10) REVERT: B 309 ARG cc_start: 0.5754 (mtm180) cc_final: 0.4567 (mmt-90) REVERT: B 320 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6225 (mt-10) REVERT: B 348 VAL cc_start: 0.8480 (t) cc_final: 0.8081 (m) REVERT: B 362 LYS cc_start: 0.7608 (mttt) cc_final: 0.7303 (mmtt) REVERT: B 408 ARG cc_start: 0.4285 (mmm160) cc_final: 0.3922 (tpm170) REVERT: B 477 MET cc_start: 0.7782 (ttm) cc_final: 0.7448 (ttt) REVERT: B 483 ASP cc_start: 0.6976 (t70) cc_final: 0.6380 (m-30) REVERT: B 523 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7584 (mt-10) outliers start: 22 outliers final: 18 residues processed: 181 average time/residue: 0.1979 time to fit residues: 48.1413 Evaluate side-chains 181 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 0.0050 chunk 31 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.164393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134055 restraints weight = 10009.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.137077 restraints weight = 6753.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139034 restraints weight = 5326.801| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7460 Z= 0.181 Angle : 0.570 12.928 10160 Z= 0.286 Chirality : 0.042 0.391 1200 Planarity : 0.004 0.057 1256 Dihedral : 3.293 12.511 1002 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.74 % Allowed : 18.28 % Favored : 78.98 % 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: 2.48 (0.28), residues: 940 helix: 2.44 (0.19), residues: 704 sheet: None (None), residues: 0 loop : -0.92 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 444 HIS 0.006 0.002 HIS B 210 PHE 0.028 0.001 PHE A 279 TYR 0.022 0.002 TYR A 134 ARG 0.005 0.001 ARG B 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1811.78 seconds wall clock time: 33 minutes 39.03 seconds (2019.03 seconds total)