Starting phenix.real_space_refine on Wed Feb 14 10:58:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpa_14852/02_2024/7zpa_14852_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpa_14852/02_2024/7zpa_14852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpa_14852/02_2024/7zpa_14852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpa_14852/02_2024/7zpa_14852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpa_14852/02_2024/7zpa_14852_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpa_14852/02_2024/7zpa_14852_updated.pdb" } resolution = 3.9 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= 0.008 sd= 0.925 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 18 5.16 5 C 5544 2.51 5 N 1574 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B GLU 413": "OE1" <-> "OE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9121 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 431, 3530 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 431, 3530 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3605 Chain: "B" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3636 Classifications: {'peptide': 443} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 972 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Time building chain proxies: 6.84, per 1000 atoms: 0.75 Number of scatterers: 9121 At special positions: 0 Unit cell: (83.566, 101.346, 136.906, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 97 15.00 O 1888 8.00 N 1574 7.00 C 5544 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: 4.57 Conformation dependent library (CDL) restraints added in 2.0 seconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 9 sheets defined 40.6% alpha, 8.6% beta 12 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 4.480A pdb=" N TYR A 21 " --> pdb=" O TYR A 17 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU A 27 " --> pdb=" O HIS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.578A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.779A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 205 through 211 removed outlier: 4.344A pdb=" N HIS A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.936A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 380 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 448 through 462 removed outlier: 3.889A pdb=" N LEU A 451 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU A 452 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 30 removed outlier: 4.711A pdb=" N TYR B 21 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.876A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 163 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 177 through 189 removed outlier: 4.122A pdb=" N LEU B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 removed outlier: 4.654A pdb=" N HIS B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 324 through 333 Processing helix chain 'B' and resid 343 through 354 Processing helix chain 'B' and resid 357 through 381 Processing helix chain 'B' and resid 408 through 418 Processing helix chain 'B' and resid 448 through 461 removed outlier: 3.554A pdb=" N LEU B 451 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU B 452 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 69 through 72 removed outlier: 3.991A pdb=" N GLY A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.609A pdb=" N GLY A 175 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 215 through 219 removed outlier: 7.432A pdb=" N VAL A 238 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N GLU A 198 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N TYR A 240 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N TYR A 272 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N THR A 241 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 274 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.815A pdb=" N LEU A 388 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 401 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 69 through 71 Processing sheet with id= F, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.592A pdb=" N GLY B 175 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 194 through 196 removed outlier: 6.467A pdb=" N ASP B 215 " --> pdb=" O TYR B 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 removed outlier: 7.358A pdb=" N TYR B 272 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR B 241 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 274 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 387 through 389 removed outlier: 3.643A pdb=" N LEU B 388 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 401 " --> pdb=" O LEU B 388 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2305 1.33 - 1.45: 2293 1.45 - 1.57: 4711 1.57 - 1.69: 190 1.69 - 1.81: 32 Bond restraints: 9531 Sorted by residual: bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.730 1.542 0.188 2.00e-02 2.50e+03 8.83e+01 bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.730 1.546 0.184 2.00e-02 2.50e+03 8.50e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.313 1.432 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.313 1.432 -0.119 2.00e-02 2.50e+03 3.51e+01 bond pdb=" OP2 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.586 1.477 0.109 2.00e-02 2.50e+03 3.00e+01 ... (remaining 9526 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.71: 784 106.71 - 113.54: 5135 113.54 - 120.38: 3816 120.38 - 127.21: 3346 127.21 - 134.05: 235 Bond angle restraints: 13316 Sorted by residual: angle pdb=" N VAL B 297 " pdb=" CA VAL B 297 " pdb=" C VAL B 297 " ideal model delta sigma weight residual 113.53 107.41 6.12 9.80e-01 1.04e+00 3.89e+01 angle pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " pdb=" C4 LLP B 309 " ideal model delta sigma weight residual 120.00 107.75 12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C GLU B 66 " pdb=" N GLY B 67 " pdb=" CA GLY B 67 " ideal model delta sigma weight residual 122.69 116.68 6.01 1.59e+00 3.96e-01 1.43e+01 angle pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " pdb=" C4 LLP A 309 " ideal model delta sigma weight residual 120.00 109.00 11.00 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA ARG B 316 " pdb=" C ARG B 316 " pdb=" O ARG B 316 " ideal model delta sigma weight residual 122.44 117.71 4.73 1.32e+00 5.74e-01 1.28e+01 ... (remaining 13311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.43: 4953 28.43 - 56.86: 471 56.86 - 85.28: 48 85.28 - 113.71: 5 113.71 - 142.14: 2 Dihedral angle restraints: 5479 sinusoidal: 2895 harmonic: 2584 Sorted by residual: dihedral pdb=" CG LLP B 309 " pdb=" CD LLP B 309 " pdb=" CE LLP B 309 " pdb=" NZ LLP B 309 " ideal model delta sinusoidal sigma weight residual 119.81 -22.33 142.14 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" CA ARG A 74 " pdb=" C ARG A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA GLU B 83 " pdb=" C GLU B 83 " pdb=" N ASP B 84 " pdb=" CA ASP B 84 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 979 0.032 - 0.064: 320 0.064 - 0.097: 104 0.097 - 0.129: 50 0.129 - 0.161: 8 Chirality restraints: 1461 Sorted by residual: chirality pdb=" CB ILE B 273 " pdb=" CA ILE B 273 " pdb=" CG1 ILE B 273 " pdb=" CG2 ILE B 273 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA GLU B 154 " pdb=" N GLU B 154 " pdb=" C GLU B 154 " pdb=" CB GLU B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CB VAL A 315 " pdb=" CA VAL A 315 " pdb=" CG1 VAL A 315 " pdb=" CG2 VAL A 315 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1458 not shown) Planarity restraints: 1363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " 0.159 2.00e-02 2.50e+03 2.67e-01 7.10e+02 pdb=" NZ LLP A 309 " -0.359 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " -0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " 0.335 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 309 " 0.078 2.00e-02 2.50e+03 7.41e-02 5.49e+01 pdb=" NZ LLP B 309 " -0.082 2.00e-02 2.50e+03 pdb=" C4 LLP B 309 " 0.070 2.00e-02 2.50e+03 pdb=" C4' LLP B 309 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 247 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 248 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " 0.024 5.00e-02 4.00e+02 ... (remaining 1360 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1181 2.75 - 3.29: 8898 3.29 - 3.83: 15282 3.83 - 4.36: 16970 4.36 - 4.90: 27545 Nonbonded interactions: 69876 Sorted by model distance: nonbonded pdb=" OG1 THR B 168 " pdb=" OE1 GLN B 171 " model vdw 2.214 2.440 nonbonded pdb=" OG SER A 308 " pdb=" O ILE A 312 " model vdw 2.221 2.440 nonbonded pdb=" OE1 GLN B 184 " pdb=" OH TYR B 330 " model vdw 2.241 2.440 nonbonded pdb=" OH TYR B 240 " pdb=" OD2 ASP B 276 " model vdw 2.244 2.440 nonbonded pdb=" OG SER B 162 " pdb=" OE2 GLU B 281 " model vdw 2.284 2.440 ... (remaining 69871 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' and (resid 15 through 81 or resid 103 through 442 or resid 444 throug \ h 464)) selection = (chain 'B' and (resid 15 through 81 or resid 84 or resid 104 through 442 or resi \ d 444 through 464)) } 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=0.50 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.000 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 31.950 Find NCS groups from input model: 0.460 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.006 0.188 9531 Z= 0.418 Angle : 0.664 12.251 13316 Z= 0.370 Chirality : 0.040 0.161 1461 Planarity : 0.009 0.267 1363 Dihedral : 19.797 142.138 3825 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.29), residues: 861 helix: 0.90 (0.28), residues: 370 sheet: -0.29 (0.50), residues: 107 loop : -1.43 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.003 0.001 HIS A 23 PHE 0.020 0.002 PHE A 128 TYR 0.018 0.002 TYR A 337 ARG 0.005 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7701 (ttm170) cc_final: 0.7443 (ttm-80) REVERT: A 291 SER cc_start: 0.7372 (m) cc_final: 0.7086 (m) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1952 time to fit residues: 24.8270 Evaluate side-chains 66 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9531 Z= 0.205 Angle : 0.622 7.772 13316 Z= 0.345 Chirality : 0.042 0.147 1461 Planarity : 0.005 0.046 1363 Dihedral : 21.621 138.703 2069 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.55 % Allowed : 7.87 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.29), residues: 861 helix: 0.79 (0.28), residues: 371 sheet: -0.70 (0.47), residues: 116 loop : -1.43 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.003 0.001 HIS A 23 PHE 0.016 0.002 PHE A 128 TYR 0.026 0.001 TYR B 21 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.933 Fit side-chains REVERT: A 32 ARG cc_start: 0.7755 (ttm170) cc_final: 0.7540 (ttm-80) REVERT: A 291 SER cc_start: 0.7363 (m) cc_final: 0.7122 (m) REVERT: A 413 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7743 (tp30) REVERT: B 195 TYR cc_start: 0.6687 (m-80) cc_final: 0.6471 (m-80) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 0.2068 time to fit residues: 22.6107 Evaluate side-chains 73 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 416 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 8.9990 chunk 26 optimal weight: 0.0020 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 overall best weight: 2.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 183 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9531 Z= 0.268 Angle : 0.658 7.423 13316 Z= 0.365 Chirality : 0.043 0.163 1461 Planarity : 0.005 0.046 1363 Dihedral : 21.981 140.333 2069 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.06 % Allowed : 12.39 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.29), residues: 861 helix: 0.61 (0.28), residues: 372 sheet: -0.99 (0.46), residues: 120 loop : -1.45 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 124 HIS 0.006 0.001 HIS A 160 PHE 0.016 0.002 PHE A 352 TYR 0.023 0.002 TYR B 21 ARG 0.003 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.916 Fit side-chains REVERT: A 32 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7519 (ttm-80) REVERT: A 291 SER cc_start: 0.7425 (m) cc_final: 0.7145 (m) outliers start: 16 outliers final: 10 residues processed: 79 average time/residue: 0.1805 time to fit residues: 21.3564 Evaluate side-chains 76 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 353 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9531 Z= 0.255 Angle : 0.633 7.637 13316 Z= 0.352 Chirality : 0.042 0.161 1461 Planarity : 0.005 0.046 1363 Dihedral : 22.096 140.603 2069 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.45 % Allowed : 15.61 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.29), residues: 861 helix: 0.53 (0.28), residues: 372 sheet: -0.84 (0.47), residues: 113 loop : -1.52 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 264 HIS 0.005 0.001 HIS A 160 PHE 0.015 0.002 PHE A 352 TYR 0.024 0.002 TYR B 21 ARG 0.003 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 0.947 Fit side-chains REVERT: A 32 ARG cc_start: 0.7703 (ttm170) cc_final: 0.7474 (ttm-80) REVERT: A 291 SER cc_start: 0.7460 (m) cc_final: 0.7168 (m) REVERT: A 413 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7698 (tp30) outliers start: 19 outliers final: 12 residues processed: 82 average time/residue: 0.1981 time to fit residues: 23.8094 Evaluate side-chains 77 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 350 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 256 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9531 Z= 0.292 Angle : 0.664 7.616 13316 Z= 0.367 Chirality : 0.043 0.166 1461 Planarity : 0.005 0.047 1363 Dihedral : 22.349 140.266 2069 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.84 % Allowed : 17.55 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.28), residues: 861 helix: 0.47 (0.28), residues: 371 sheet: -0.94 (0.47), residues: 111 loop : -1.58 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 124 HIS 0.008 0.002 HIS A 145 PHE 0.017 0.002 PHE A 352 TYR 0.024 0.002 TYR B 21 ARG 0.006 0.001 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 0.967 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 80 average time/residue: 0.1846 time to fit residues: 22.3154 Evaluate side-chains 77 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9531 Z= 0.339 Angle : 0.697 6.996 13316 Z= 0.384 Chirality : 0.045 0.221 1461 Planarity : 0.005 0.047 1363 Dihedral : 22.719 139.665 2069 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.48 % Allowed : 17.94 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.14 (0.28), residues: 861 helix: 0.28 (0.27), residues: 372 sheet: -1.28 (0.46), residues: 119 loop : -1.61 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 264 HIS 0.007 0.002 HIS A 160 PHE 0.019 0.003 PHE A 352 TYR 0.023 0.002 TYR B 21 ARG 0.005 0.001 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 0.926 Fit side-chains REVERT: A 307 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7820 (t80) outliers start: 25 outliers final: 16 residues processed: 80 average time/residue: 0.1818 time to fit residues: 21.8166 Evaluate side-chains 76 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9531 Z= 0.286 Angle : 0.647 6.882 13316 Z= 0.359 Chirality : 0.043 0.212 1461 Planarity : 0.005 0.050 1363 Dihedral : 22.678 139.121 2069 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.97 % Allowed : 19.23 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.29), residues: 861 helix: 0.43 (0.28), residues: 372 sheet: -1.06 (0.47), residues: 112 loop : -1.59 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 264 HIS 0.005 0.001 HIS A 160 PHE 0.016 0.002 PHE A 352 TYR 0.018 0.002 TYR A 319 ARG 0.003 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 64 time to evaluate : 0.977 Fit side-chains REVERT: A 307 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7772 (t80) outliers start: 21 outliers final: 15 residues processed: 80 average time/residue: 0.1817 time to fit residues: 21.7747 Evaluate side-chains 78 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 83 optimal weight: 0.0470 chunk 87 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9531 Z= 0.202 Angle : 0.588 7.145 13316 Z= 0.327 Chirality : 0.040 0.155 1461 Planarity : 0.005 0.052 1363 Dihedral : 22.591 139.867 2069 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.97 % Allowed : 19.87 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.29), residues: 861 helix: 0.61 (0.28), residues: 373 sheet: -0.94 (0.47), residues: 113 loop : -1.54 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 124 HIS 0.004 0.001 HIS A 160 PHE 0.012 0.002 PHE A 128 TYR 0.018 0.001 TYR B 21 ARG 0.003 0.000 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.947 Fit side-chains REVERT: A 307 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7549 (t80) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 0.1742 time to fit residues: 22.0178 Evaluate side-chains 81 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 449 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9531 Z= 0.221 Angle : 0.614 8.784 13316 Z= 0.337 Chirality : 0.041 0.162 1461 Planarity : 0.005 0.054 1363 Dihedral : 22.624 139.831 2069 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.97 % Allowed : 20.52 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.29), residues: 861 helix: 0.62 (0.28), residues: 372 sheet: -0.91 (0.47), residues: 112 loop : -1.57 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 264 HIS 0.007 0.001 HIS A 145 PHE 0.012 0.002 PHE A 352 TYR 0.018 0.001 TYR B 21 ARG 0.003 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.988 Fit side-chains REVERT: A 307 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7595 (t80) REVERT: A 413 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7801 (tp30) outliers start: 21 outliers final: 18 residues processed: 80 average time/residue: 0.1905 time to fit residues: 22.6144 Evaluate side-chains 83 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 449 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 0.0870 chunk 94 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 23 optimal weight: 0.0040 overall best weight: 0.5574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9531 Z= 0.161 Angle : 0.579 8.978 13316 Z= 0.317 Chirality : 0.039 0.155 1461 Planarity : 0.005 0.054 1363 Dihedral : 22.479 140.351 2069 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.42 % Allowed : 22.06 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.29), residues: 861 helix: 0.77 (0.28), residues: 372 sheet: -0.89 (0.48), residues: 105 loop : -1.49 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 124 HIS 0.003 0.001 HIS B 110 PHE 0.011 0.001 PHE A 77 TYR 0.017 0.001 TYR B 21 ARG 0.003 0.000 ARG B 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8528 (tmtt) cc_final: 0.8197 (tptp) REVERT: A 307 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7450 (t80) REVERT: A 413 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7922 (tp30) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.1843 time to fit residues: 21.0753 Evaluate side-chains 76 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 337 TYR Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 75 optimal weight: 0.0020 chunk 31 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.0040 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.121254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096040 restraints weight = 21057.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098196 restraints weight = 12059.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.099675 restraints weight = 8040.970| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9531 Z= 0.159 Angle : 0.576 9.044 13316 Z= 0.315 Chirality : 0.039 0.147 1461 Planarity : 0.005 0.051 1363 Dihedral : 22.405 140.530 2069 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.55 % Allowed : 21.94 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.29), residues: 861 helix: 0.88 (0.28), residues: 372 sheet: -1.08 (0.47), residues: 100 loop : -1.41 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 124 HIS 0.005 0.001 HIS B 110 PHE 0.011 0.001 PHE A 128 TYR 0.018 0.001 TYR B 21 ARG 0.003 0.000 ARG B 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1706.46 seconds wall clock time: 31 minutes 51.28 seconds (1911.28 seconds total)