Starting phenix.real_space_refine on Sat Apr 6 03:35:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8h_36070/04_2024/8j8h_36070.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8h_36070/04_2024/8j8h_36070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8h_36070/04_2024/8j8h_36070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8h_36070/04_2024/8j8h_36070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8h_36070/04_2024/8j8h_36070.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8h_36070/04_2024/8j8h_36070.pdb" } resolution = 3.4 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= 0.016 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: 6 Type Number sf(0) Gaussians P 39 5.49 5 Mg 1 5.21 5 S 18 5.16 5 C 4316 2.51 5 N 1167 2.21 5 O 1327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "B PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6868 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3651 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 25, 'TRANS': 426} Chain breaks: 1 Chain: "B" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2421 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain: "E" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 403 Classifications: {'DNA': 13, 'RNA': 7} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 19} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 392 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.28, per 1000 atoms: 0.62 Number of scatterers: 6868 At special positions: 0 Unit cell: (84, 79.8, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 39 15.00 Mg 1 11.99 O 1327 8.00 N 1167 7.00 C 4316 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: 3.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 11 sheets defined 31.8% alpha, 15.6% beta 10 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.747A pdb=" N ALA A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 61 removed outlier: 3.641A pdb=" N LYS A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.546A pdb=" N ILE A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 removed outlier: 4.050A pdb=" N TYR A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.496A pdb=" N ARG A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.188A pdb=" N SER A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 451 through 463 removed outlier: 3.591A pdb=" N VAL A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 456 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 4.211A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 155 removed outlier: 3.899A pdb=" N SER B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.597A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.510A pdb=" N PHE B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 366 removed outlier: 3.510A pdb=" N GLY B 365 " --> pdb=" O ARG B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.562A pdb=" N PHE B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 282 removed outlier: 7.119A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE A 412 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU A 3 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS A 2 " --> pdb=" O PHE B 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.892A pdb=" N LYS A 270 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 removed outlier: 5.827A pdb=" N SER A 41 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 141 " --> pdb=" O LEU A 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 303 Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.684A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.532A pdb=" N VAL B 334 " --> pdb=" O LYS B 328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 286 Processing sheet with id=AB1, first strand: chain 'B' and resid 283 through 286 Processing sheet with id=AB2, first strand: chain 'B' and resid 390 through 394 197 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1718 1.33 - 1.45: 1554 1.45 - 1.57: 3745 1.57 - 1.69: 77 1.69 - 1.81: 28 Bond restraints: 7122 Sorted by residual: bond pdb=" CB PRO B 419 " pdb=" CG PRO B 419 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 9.98e+00 bond pdb=" CB PRO A 241 " pdb=" CG PRO A 241 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.00e+00 bond pdb=" CG PRO A 241 " pdb=" CD PRO A 241 " ideal model delta sigma weight residual 1.503 1.455 0.048 3.40e-02 8.65e+02 1.99e+00 bond pdb=" CB ASP B 346 " pdb=" CG ASP B 346 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.57e+00 bond pdb=" C SER B 180 " pdb=" N PHE B 181 " ideal model delta sigma weight residual 1.333 1.301 0.031 2.74e-02 1.33e+03 1.32e+00 ... (remaining 7117 not shown) Histogram of bond angle deviations from ideal: 97.08 - 104.48: 239 104.48 - 111.88: 3421 111.88 - 119.28: 2418 119.28 - 126.69: 3481 126.69 - 134.09: 228 Bond angle restraints: 9787 Sorted by residual: angle pdb=" CA PRO B 419 " pdb=" N PRO B 419 " pdb=" CD PRO B 419 " ideal model delta sigma weight residual 112.00 99.90 12.10 1.40e+00 5.10e-01 7.47e+01 angle pdb=" CA PRO A 241 " pdb=" N PRO A 241 " pdb=" CD PRO A 241 " ideal model delta sigma weight residual 112.00 105.55 6.45 1.40e+00 5.10e-01 2.12e+01 angle pdb=" CA LEU A 394 " pdb=" CB LEU A 394 " pdb=" CG LEU A 394 " ideal model delta sigma weight residual 116.30 130.85 -14.55 3.50e+00 8.16e-02 1.73e+01 angle pdb=" N PRO A 241 " pdb=" CD PRO A 241 " pdb=" CG PRO A 241 " ideal model delta sigma weight residual 103.20 97.08 6.12 1.50e+00 4.44e-01 1.67e+01 angle pdb=" CA LEU A 215 " pdb=" CB LEU A 215 " pdb=" CG LEU A 215 " ideal model delta sigma weight residual 116.30 129.09 -12.79 3.50e+00 8.16e-02 1.34e+01 ... (remaining 9782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.87: 3797 28.87 - 57.75: 384 57.75 - 86.62: 29 86.62 - 115.49: 2 115.49 - 144.37: 3 Dihedral angle restraints: 4215 sinusoidal: 2047 harmonic: 2168 Sorted by residual: dihedral pdb=" C4' DA F 9 " pdb=" C3' DA F 9 " pdb=" O3' DA F 9 " pdb=" P A DG F 10 " ideal model delta sinusoidal sigma weight residual 220.00 75.63 144.37 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA LYS B 328 " pdb=" C LYS B 328 " pdb=" N LEU B 329 " pdb=" CA LEU B 329 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C4' DA F 16 " pdb=" C3' DA F 16 " pdb=" O3' DA F 16 " pdb=" P DG F 17 " ideal model delta sinusoidal sigma weight residual 220.00 82.66 137.34 1 3.50e+01 8.16e-04 1.36e+01 ... (remaining 4212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 857 0.054 - 0.108: 163 0.108 - 0.162: 25 0.162 - 0.215: 1 0.215 - 0.269: 4 Chirality restraints: 1050 Sorted by residual: chirality pdb=" CB ILE A 219 " pdb=" CA ILE A 219 " pdb=" CG1 ILE A 219 " pdb=" CG2 ILE A 219 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1' U E 17 " pdb=" O4' U E 17 " pdb=" C2' U E 17 " pdb=" N1 U E 17 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1' U E 1 " pdb=" O4' U E 1 " pdb=" C2' U E 1 " pdb=" N1 U E 1 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1047 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 418 " 0.056 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO B 419 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 419 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 419 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 240 " -0.040 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 241 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 320 " -0.014 2.00e-02 2.50e+03 1.33e-02 4.41e+00 pdb=" CG TRP A 320 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 320 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 320 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 320 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 320 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 320 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 320 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 320 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 320 " -0.001 2.00e-02 2.50e+03 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 81 2.51 - 3.11: 5082 3.11 - 3.71: 11814 3.71 - 4.30: 15642 4.30 - 4.90: 24702 Nonbonded interactions: 57321 Sorted by model distance: nonbonded pdb=" OP1 A E 3 " pdb="MG MG A 601 " model vdw 1.914 2.170 nonbonded pdb=" ND2 ASN A 468 " pdb="MG MG A 601 " model vdw 2.096 2.250 nonbonded pdb=" OG SER A 11 " pdb=" O CYS A 20 " model vdw 2.234 2.440 nonbonded pdb=" OD1 ASN A 468 " pdb="MG MG A 601 " model vdw 2.238 2.170 nonbonded pdb=" O TYR A 328 " pdb=" ND1 HIS A 329 " model vdw 2.254 2.520 ... (remaining 57316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.60 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 3.670 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.940 Find NCS groups from input model: 0.180 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 0.158 7122 Z= 0.250 Angle : 0.694 14.547 9787 Z= 0.335 Chirality : 0.045 0.269 1050 Planarity : 0.005 0.079 1106 Dihedral : 20.214 144.365 2817 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.61 % Allowed : 33.69 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.31), residues: 732 helix: -0.66 (0.39), residues: 185 sheet: -0.98 (0.44), residues: 140 loop : -1.17 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 320 HIS 0.003 0.000 HIS A 217 PHE 0.017 0.001 PHE B 411 TYR 0.017 0.001 TYR B 416 ARG 0.002 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.765 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 86 average time/residue: 0.1500 time to fit residues: 18.9074 Evaluate side-chains 83 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 349 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.0000 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN B 364 GLN B 370 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 7122 Z= 0.262 Angle : 0.662 11.617 9787 Z= 0.326 Chirality : 0.046 0.284 1050 Planarity : 0.004 0.048 1106 Dihedral : 18.737 144.558 1280 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.77 % Allowed : 28.53 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.29), residues: 732 helix: -0.86 (0.33), residues: 211 sheet: -0.97 (0.43), residues: 145 loop : -1.42 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 320 HIS 0.003 0.001 HIS A 217 PHE 0.020 0.001 PHE B 411 TYR 0.021 0.001 TYR A 104 ARG 0.002 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 87 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.6648 (pmm) cc_final: 0.6397 (pmm) REVERT: A 139 TRP cc_start: 0.8681 (m100) cc_final: 0.7116 (m100) REVERT: A 213 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7630 (mtt180) REVERT: A 289 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: A 444 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 476 GLU cc_start: 0.7779 (pm20) cc_final: 0.7565 (pm20) REVERT: B 416 TYR cc_start: 0.8551 (p90) cc_final: 0.8345 (p90) outliers start: 38 outliers final: 18 residues processed: 109 average time/residue: 0.2328 time to fit residues: 35.3834 Evaluate side-chains 104 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 329 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7122 Z= 0.203 Angle : 0.637 11.562 9787 Z= 0.308 Chirality : 0.046 0.291 1050 Planarity : 0.004 0.045 1106 Dihedral : 18.519 143.455 1277 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 5.01 % Allowed : 29.14 % Favored : 65.86 % 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: -1.76 (0.30), residues: 732 helix: -0.77 (0.33), residues: 213 sheet: -1.00 (0.44), residues: 142 loop : -1.41 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 320 HIS 0.002 0.000 HIS A 217 PHE 0.021 0.001 PHE B 411 TYR 0.021 0.001 TYR A 104 ARG 0.002 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 89 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6656 (pmm) cc_final: 0.6432 (pmm) REVERT: A 289 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: A 394 LEU cc_start: 0.8322 (tt) cc_final: 0.8116 (tt) REVERT: A 444 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7614 (tm-30) REVERT: A 476 GLU cc_start: 0.7843 (pm20) cc_final: 0.7620 (pm20) REVERT: B 336 MET cc_start: 0.7722 (tpp) cc_final: 0.7397 (tpp) outliers start: 33 outliers final: 21 residues processed: 108 average time/residue: 0.1511 time to fit residues: 23.7937 Evaluate side-chains 102 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 381 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 0.0270 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7122 Z= 0.238 Angle : 0.630 12.269 9787 Z= 0.309 Chirality : 0.046 0.286 1050 Planarity : 0.004 0.043 1106 Dihedral : 18.543 144.042 1277 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.61 % Allowed : 28.98 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.30), residues: 732 helix: -0.71 (0.33), residues: 213 sheet: -1.05 (0.44), residues: 142 loop : -1.41 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 320 HIS 0.002 0.000 HIS B 320 PHE 0.020 0.001 PHE B 305 TYR 0.020 0.001 TYR A 104 ARG 0.002 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 82 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6648 (pmm) cc_final: 0.6434 (pmm) REVERT: A 289 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: A 394 LEU cc_start: 0.8213 (tt) cc_final: 0.7984 (tt) REVERT: A 444 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7414 (tm-30) REVERT: A 476 GLU cc_start: 0.7873 (pm20) cc_final: 0.7592 (pm20) REVERT: B 307 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8630 (tmtt) REVERT: B 336 MET cc_start: 0.7793 (tpp) cc_final: 0.7488 (tpp) outliers start: 37 outliers final: 24 residues processed: 107 average time/residue: 0.1545 time to fit residues: 23.8029 Evaluate side-chains 108 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 381 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.0060 chunk 41 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 7122 Z= 0.435 Angle : 0.737 11.246 9787 Z= 0.369 Chirality : 0.049 0.267 1050 Planarity : 0.005 0.047 1106 Dihedral : 18.677 145.373 1277 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 7.28 % Allowed : 28.98 % Favored : 63.73 % 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: -2.03 (0.30), residues: 732 helix: -0.87 (0.33), residues: 213 sheet: -1.47 (0.44), residues: 143 loop : -1.53 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 320 HIS 0.004 0.001 HIS A 329 PHE 0.022 0.002 PHE B 411 TYR 0.024 0.002 TYR A 104 ARG 0.004 0.001 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 75 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7508 (mtt180) REVERT: A 289 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: A 394 LEU cc_start: 0.8388 (tt) cc_final: 0.8076 (tt) REVERT: A 444 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 476 GLU cc_start: 0.7764 (pm20) cc_final: 0.7440 (pm20) REVERT: A 505 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7818 (p90) REVERT: B 402 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8731 (mm) REVERT: B 414 MET cc_start: 0.6433 (mmp) cc_final: 0.6178 (mmp) outliers start: 48 outliers final: 28 residues processed: 110 average time/residue: 0.1560 time to fit residues: 24.2987 Evaluate side-chains 108 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 76 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7122 Z= 0.207 Angle : 0.641 12.297 9787 Z= 0.314 Chirality : 0.046 0.298 1050 Planarity : 0.004 0.042 1106 Dihedral : 18.493 143.778 1277 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.70 % Allowed : 31.41 % Favored : 63.88 % 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: -1.85 (0.30), residues: 732 helix: -0.67 (0.33), residues: 214 sheet: -1.33 (0.44), residues: 140 loop : -1.47 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 320 HIS 0.002 0.001 HIS B 320 PHE 0.021 0.001 PHE B 411 TYR 0.022 0.001 TYR A 104 ARG 0.002 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8904 (t0) cc_final: 0.8613 (t0) REVERT: A 104 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.6544 (t80) REVERT: A 289 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: A 444 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 476 GLU cc_start: 0.7961 (pm20) cc_final: 0.7663 (pm20) REVERT: A 505 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7922 (p90) REVERT: B 167 LYS cc_start: 0.7317 (pptt) cc_final: 0.7052 (pptt) REVERT: B 191 ASP cc_start: 0.8943 (t0) cc_final: 0.8708 (t0) REVERT: B 289 LYS cc_start: 0.8356 (mptt) cc_final: 0.8097 (mptt) REVERT: B 414 MET cc_start: 0.6246 (mmp) cc_final: 0.5995 (mmp) outliers start: 31 outliers final: 20 residues processed: 113 average time/residue: 0.1450 time to fit residues: 23.9676 Evaluate side-chains 108 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7122 Z= 0.332 Angle : 0.676 11.859 9787 Z= 0.335 Chirality : 0.047 0.277 1050 Planarity : 0.004 0.042 1106 Dihedral : 18.530 144.314 1277 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 6.22 % Allowed : 30.96 % Favored : 62.82 % 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: -2.00 (0.30), residues: 732 helix: -0.71 (0.33), residues: 214 sheet: -1.63 (0.44), residues: 143 loop : -1.52 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 320 HIS 0.003 0.001 HIS A 217 PHE 0.020 0.002 PHE B 411 TYR 0.023 0.002 TYR A 104 ARG 0.003 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 76 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7532 (tpm170) REVERT: A 104 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6383 (t80) REVERT: A 289 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: A 444 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7368 (tm-30) REVERT: A 476 GLU cc_start: 0.7852 (pm20) cc_final: 0.7499 (pm20) REVERT: A 505 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7926 (p90) REVERT: B 288 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8496 (m) REVERT: B 402 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8810 (mm) outliers start: 41 outliers final: 28 residues processed: 105 average time/residue: 0.1579 time to fit residues: 23.6899 Evaluate side-chains 110 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 76 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 0.0670 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7122 Z= 0.203 Angle : 0.667 12.145 9787 Z= 0.321 Chirality : 0.046 0.301 1050 Planarity : 0.003 0.040 1106 Dihedral : 18.418 142.700 1277 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.46 % Allowed : 31.71 % Favored : 62.82 % 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: -1.79 (0.30), residues: 732 helix: -0.60 (0.34), residues: 211 sheet: -1.28 (0.46), residues: 133 loop : -1.45 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 320 HIS 0.003 0.001 HIS B 320 PHE 0.030 0.001 PHE A 93 TYR 0.021 0.001 TYR A 104 ARG 0.002 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 90 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6374 (t80) REVERT: A 139 TRP cc_start: 0.8518 (m100) cc_final: 0.7464 (m100) REVERT: A 289 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: A 325 LYS cc_start: 0.4701 (OUTLIER) cc_final: 0.4144 (mmmt) REVERT: A 444 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7546 (tm-30) REVERT: A 476 GLU cc_start: 0.7987 (pm20) cc_final: 0.7718 (pm20) REVERT: A 505 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7944 (p90) REVERT: B 191 ASP cc_start: 0.8938 (t0) cc_final: 0.8715 (t0) REVERT: B 288 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8811 (m) REVERT: B 345 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8119 (tmm) outliers start: 36 outliers final: 24 residues processed: 112 average time/residue: 0.1660 time to fit residues: 26.0387 Evaluate side-chains 118 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 0.0060 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 75 optimal weight: 4.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7122 Z= 0.195 Angle : 0.678 12.199 9787 Z= 0.324 Chirality : 0.047 0.298 1050 Planarity : 0.004 0.040 1106 Dihedral : 18.396 141.695 1277 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.70 % Allowed : 33.08 % Favored : 62.22 % 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: -1.80 (0.30), residues: 732 helix: -0.60 (0.33), residues: 210 sheet: -1.34 (0.45), residues: 135 loop : -1.44 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 320 HIS 0.003 0.001 HIS B 320 PHE 0.020 0.001 PHE A 93 TYR 0.019 0.001 TYR A 104 ARG 0.002 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7828 (tpm170) REVERT: A 104 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.6364 (t80) REVERT: A 252 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7664 (tp) REVERT: A 289 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: A 325 LYS cc_start: 0.4528 (OUTLIER) cc_final: 0.4116 (mmmt) REVERT: A 444 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 476 GLU cc_start: 0.7938 (pm20) cc_final: 0.7627 (pm20) REVERT: A 505 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7950 (p90) REVERT: B 167 LYS cc_start: 0.6901 (pptt) cc_final: 0.6574 (pptt) outliers start: 31 outliers final: 20 residues processed: 112 average time/residue: 0.1738 time to fit residues: 27.1812 Evaluate side-chains 113 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 6 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7122 Z= 0.200 Angle : 0.673 12.006 9787 Z= 0.323 Chirality : 0.046 0.297 1050 Planarity : 0.004 0.040 1106 Dihedral : 18.370 141.317 1277 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.95 % Allowed : 33.54 % Favored : 62.52 % 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: -1.74 (0.30), residues: 732 helix: -0.57 (0.33), residues: 210 sheet: -1.28 (0.45), residues: 135 loop : -1.40 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 320 HIS 0.002 0.001 HIS B 320 PHE 0.028 0.001 PHE A 93 TYR 0.018 0.001 TYR A 104 ARG 0.001 0.000 ARG B 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7829 (tpm170) REVERT: A 289 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: A 325 LYS cc_start: 0.4538 (OUTLIER) cc_final: 0.4119 (mmmt) REVERT: A 444 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 476 GLU cc_start: 0.7952 (pm20) cc_final: 0.7630 (pm20) REVERT: A 505 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7921 (p90) REVERT: B 191 ASP cc_start: 0.8923 (t0) cc_final: 0.8698 (t0) outliers start: 26 outliers final: 22 residues processed: 108 average time/residue: 0.1798 time to fit residues: 26.8335 Evaluate side-chains 113 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.0270 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 0.0010 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 3 optimal weight: 0.0570 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.110221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088960 restraints weight = 19214.494| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 5.26 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7122 Z= 0.173 Angle : 0.674 12.010 9787 Z= 0.322 Chirality : 0.046 0.307 1050 Planarity : 0.004 0.039 1106 Dihedral : 18.342 139.714 1277 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.25 % Allowed : 33.54 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.30), residues: 732 helix: -0.51 (0.34), residues: 210 sheet: -0.82 (0.47), residues: 130 loop : -1.41 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 PHE 0.024 0.001 PHE A 93 TYR 0.016 0.001 TYR A 104 ARG 0.002 0.000 ARG B 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1725.63 seconds wall clock time: 32 minutes 29.31 seconds (1949.31 seconds total)