Starting phenix.real_space_refine on Fri Nov 15 12:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iss_35694/11_2024/8iss_35694.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iss_35694/11_2024/8iss_35694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iss_35694/11_2024/8iss_35694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iss_35694/11_2024/8iss_35694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iss_35694/11_2024/8iss_35694.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iss_35694/11_2024/8iss_35694.cif" } resolution = 3.19 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= 0.002 sd= 0.149 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 79 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 5310 2.51 5 N 1557 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8807 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 941 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "B" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1839 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain breaks: 2 Chain: "C" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2018 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 18, 'TRANS': 238} Chain breaks: 1 Chain: "D" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2298 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 21, 'TRANS': 267} Chain breaks: 1 Chain: "E" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1710 Inner-chain residues flagged as termini: ['pdbres=" A E 47 "'] Classifications: {'RNA': 80} Modifications used: {'5*END': 1, 'p5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 31, 'rna3p_pyr': 29} Link IDs: {'rna2p': 18, 'rna3p': 61} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" 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: 5.50, per 1000 atoms: 0.62 Number of scatterers: 8807 At special positions: 0 Unit cell: (74.905, 86.51, 131.875, 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 27 16.00 P 79 15.00 Mg 1 11.99 O 1833 8.00 N 1557 7.00 C 5310 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 - 3.00 Amino acid : True - 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: 2.46 Conformation dependent library (CDL) restraints added in 847.8 milliseconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 37.3% alpha, 17.3% beta 28 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 43 through 51 Processing helix chain 'A' and resid 56 through 73 Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 115 through 130 Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 400 through 414 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 456 through 460 removed outlier: 3.609A pdb=" N ARG B 459 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER B 460 " --> pdb=" O ARG B 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 460' Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.667A pdb=" N LEU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 112 Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.599A pdb=" N LYS C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 230 removed outlier: 3.707A pdb=" N ARG C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 284 Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 48 through 67 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 113 through 123 Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 151 through 164 removed outlier: 3.550A pdb=" N TYR D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.801A pdb=" N ALA D 414 " --> pdb=" O PRO D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 424 Processing helix chain 'D' and resid 454 through 459 removed outlier: 3.865A pdb=" N ALA D 459 " --> pdb=" O ASP D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 496 Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 84 removed outlier: 3.734A pdb=" N GLU A 78 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 91 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.671A pdb=" N THR A 108 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.918A pdb=" N LYS C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE C 259 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N CYS C 291 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN C 261 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR C 258 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 244 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N CYS C 262 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N GLY C 242 " --> pdb=" O CYS C 262 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 237 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE C 244 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER C 235 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL C 246 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE C 233 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 50 Processing sheet with id=AA5, first strand: chain 'B' and resid 366 through 368 removed outlier: 4.114A pdb=" N TYR B 380 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 418 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU D 504 " --> pdb=" O SER D 511 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE D 515 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU D 500 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA D 471 " --> pdb=" O ASP D 451 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASP D 451 " --> pdb=" O ALA D 471 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET D 473 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 386 through 388 removed outlier: 4.066A pdb=" N LEU B 418 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 52 removed outlier: 4.195A pdb=" N SER C 11 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 12 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 5 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 4 " --> pdb=" O THR C 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 187 removed outlier: 4.395A pdb=" N ARG D 70 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 195 through 197 removed outlier: 3.566A pdb=" N VAL C 195 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 104 through 106 removed outlier: 5.010A pdb=" N GLN D 110 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL D 78 " --> pdb=" O HIS D 127 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2461 1.34 - 1.45: 1946 1.45 - 1.57: 4569 1.57 - 1.69: 157 1.69 - 1.81: 43 Bond restraints: 9176 Sorted by residual: bond pdb=" C ASP A 132 " pdb=" N PRO A 133 " ideal model delta sigma weight residual 1.326 1.339 -0.013 1.44e-02 4.82e+03 7.58e-01 bond pdb=" C ALA B 8 " pdb=" N PRO B 9 " ideal model delta sigma weight residual 1.335 1.342 -0.007 8.70e-03 1.32e+04 7.27e-01 bond pdb=" CG LYS B 330 " pdb=" CD LYS B 330 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.02e-01 bond pdb=" CB LYS B 330 " pdb=" CG LYS B 330 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.83e-01 bond pdb=" CD LYS B 330 " pdb=" CE LYS B 330 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.54e-01 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 12709 2.28 - 4.56: 100 4.56 - 6.84: 4 6.84 - 9.12: 1 9.12 - 11.40: 1 Bond angle restraints: 12815 Sorted by residual: angle pdb=" CG LYS D 32 " pdb=" CD LYS D 32 " pdb=" CE LYS D 32 " ideal model delta sigma weight residual 111.30 122.70 -11.40 2.30e+00 1.89e-01 2.46e+01 angle pdb=" CB LYS B 330 " pdb=" CG LYS B 330 " pdb=" CD LYS B 330 " ideal model delta sigma weight residual 111.30 118.42 -7.12 2.30e+00 1.89e-01 9.60e+00 angle pdb=" C LEU C 113 " pdb=" N GLU C 114 " pdb=" CA GLU C 114 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.69e+00 angle pdb=" CA TYR B 343 " pdb=" CB TYR B 343 " pdb=" CG TYR B 343 " ideal model delta sigma weight residual 113.90 109.49 4.41 1.80e+00 3.09e-01 6.02e+00 angle pdb=" C TYR B 318 " pdb=" N GLU B 319 " pdb=" CA GLU B 319 " ideal model delta sigma weight residual 121.54 125.89 -4.35 1.91e+00 2.74e-01 5.19e+00 ... (remaining 12810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.10: 4706 19.10 - 38.19: 616 38.19 - 57.29: 207 57.29 - 76.38: 103 76.38 - 95.48: 14 Dihedral angle restraints: 5646 sinusoidal: 3065 harmonic: 2581 Sorted by residual: dihedral pdb=" CA LYS B 320 " pdb=" C LYS B 320 " pdb=" N GLU B 321 " pdb=" CA GLU B 321 " ideal model delta harmonic sigma weight residual 180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ILE D 510 " pdb=" C ILE D 510 " pdb=" N SER D 511 " pdb=" CA SER D 511 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA PHE D 502 " pdb=" C PHE D 502 " pdb=" N ALA D 503 " pdb=" CA ALA D 503 " ideal model delta harmonic sigma weight residual 180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1016 0.028 - 0.057: 320 0.057 - 0.085: 66 0.085 - 0.113: 58 0.113 - 0.142: 18 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CA VAL B 355 " pdb=" N VAL B 355 " pdb=" C VAL B 355 " pdb=" CB VAL B 355 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA VAL D 482 " pdb=" N VAL D 482 " pdb=" C VAL D 482 " pdb=" CB VAL D 482 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE C 259 " pdb=" N ILE C 259 " pdb=" C ILE C 259 " pdb=" CB ILE C 259 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1475 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 114 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLU C 114 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU C 114 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS C 115 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 39 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO D 40 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 40 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 40 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 372 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO B 373 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.020 5.00e-02 4.00e+02 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 138 2.60 - 3.18: 7492 3.18 - 3.75: 14396 3.75 - 4.33: 19760 4.33 - 4.90: 32234 Nonbonded interactions: 74020 Sorted by model distance: nonbonded pdb=" O2' G E 50 " pdb=" OP2 U E 54 " model vdw 2.026 3.040 nonbonded pdb=" O GLY A 158 " pdb=" OG SER C 303 " model vdw 2.042 3.040 nonbonded pdb=" OP2 G E 12 " pdb="MG MG E 101 " model vdw 2.051 2.170 nonbonded pdb=" O2' C E 35 " pdb=" O3' G E 38 " model vdw 2.071 3.040 nonbonded pdb=" O2' C E 35 " pdb=" O2' G E 38 " model vdw 2.091 3.040 ... (remaining 74015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.340 Find NCS groups from input model: 0.130 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9176 Z= 0.164 Angle : 0.514 11.398 12815 Z= 0.264 Chirality : 0.036 0.142 1478 Planarity : 0.004 0.044 1344 Dihedral : 20.029 95.477 3978 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.39 % Allowed : 22.51 % Favored : 77.09 % 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: -1.16 (0.29), residues: 873 helix: 0.81 (0.30), residues: 316 sheet: -2.26 (0.40), residues: 165 loop : -1.34 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 99 HIS 0.003 0.001 HIS C 255 PHE 0.010 0.001 PHE D 512 TYR 0.017 0.001 TYR D 155 ARG 0.008 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.876 Fit side-chains REVERT: B 11 ARG cc_start: 0.6382 (ttm110) cc_final: 0.5869 (mtp85) outliers start: 3 outliers final: 3 residues processed: 102 average time/residue: 0.2943 time to fit residues: 38.9835 Evaluate side-chains 93 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 478 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.0040 chunk 55 optimal weight: 0.1980 chunk 86 optimal weight: 0.3980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9176 Z= 0.163 Angle : 0.544 6.352 12815 Z= 0.277 Chirality : 0.038 0.198 1478 Planarity : 0.004 0.044 1344 Dihedral : 18.476 92.237 2233 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.01 % Allowed : 20.81 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.30), residues: 873 helix: 1.42 (0.31), residues: 300 sheet: -1.84 (0.42), residues: 157 loop : -0.92 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 99 HIS 0.003 0.001 HIS C 255 PHE 0.012 0.001 PHE A 139 TYR 0.015 0.002 TYR B 343 ARG 0.008 0.001 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.899 Fit side-chains REVERT: A 47 LEU cc_start: 0.6824 (mm) cc_final: 0.6610 (mm) REVERT: A 49 MET cc_start: 0.6416 (mpp) cc_final: 0.5894 (mpp) REVERT: A 71 MET cc_start: 0.6222 (mmm) cc_final: 0.5668 (mmm) REVERT: A 145 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: B 11 ARG cc_start: 0.6373 (ttm110) cc_final: 0.5872 (mtp85) REVERT: B 44 MET cc_start: 0.7500 (ttt) cc_final: 0.7241 (ttt) REVERT: C 45 ARG cc_start: 0.7490 (ttt180) cc_final: 0.7233 (mtt-85) REVERT: C 103 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5335 (mp0) REVERT: C 272 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: D 22 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7579 (mt-10) REVERT: D 85 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6585 (pm20) outliers start: 23 outliers final: 6 residues processed: 123 average time/residue: 0.2527 time to fit residues: 41.4602 Evaluate side-chains 95 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 58 optimal weight: 0.0570 chunk 23 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9176 Z= 0.174 Angle : 0.516 6.253 12815 Z= 0.262 Chirality : 0.037 0.147 1478 Planarity : 0.004 0.045 1344 Dihedral : 18.272 90.542 2232 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.01 % Allowed : 20.94 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.30), residues: 873 helix: 1.38 (0.31), residues: 308 sheet: -1.69 (0.41), residues: 163 loop : -0.84 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 82 HIS 0.003 0.001 HIS C 257 PHE 0.013 0.001 PHE A 139 TYR 0.016 0.002 TYR B 343 ARG 0.008 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6585 (mm) cc_final: 0.6185 (mm) REVERT: A 71 MET cc_start: 0.6118 (mmm) cc_final: 0.5618 (mmm) REVERT: A 145 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: B 11 ARG cc_start: 0.6262 (ttm110) cc_final: 0.5795 (mtp85) REVERT: B 44 MET cc_start: 0.7489 (ttt) cc_final: 0.7280 (ttt) REVERT: C 45 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7238 (mtt-85) REVERT: C 272 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7259 (mm-40) REVERT: D 85 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6601 (pm20) outliers start: 23 outliers final: 11 residues processed: 117 average time/residue: 0.2777 time to fit residues: 42.5400 Evaluate side-chains 105 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9176 Z= 0.239 Angle : 0.545 6.858 12815 Z= 0.275 Chirality : 0.038 0.139 1478 Planarity : 0.004 0.048 1344 Dihedral : 18.341 90.646 2232 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.27 % Allowed : 21.60 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.30), residues: 873 helix: 1.32 (0.30), residues: 307 sheet: -1.59 (0.42), residues: 162 loop : -0.80 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 82 HIS 0.004 0.001 HIS C 257 PHE 0.014 0.002 PHE A 139 TYR 0.018 0.002 TYR B 343 ARG 0.010 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6109 (mm) REVERT: A 71 MET cc_start: 0.6253 (mmm) cc_final: 0.5700 (mmm) REVERT: A 145 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: B 44 MET cc_start: 0.7520 (ttt) cc_final: 0.7294 (ttt) REVERT: B 435 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6374 (mp0) REVERT: D 85 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: D 172 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6964 (tt0) outliers start: 25 outliers final: 15 residues processed: 119 average time/residue: 0.2492 time to fit residues: 39.4320 Evaluate side-chains 115 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP 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: 3.9990 chunk 1 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 78 optimal weight: 0.0770 chunk 63 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9176 Z= 0.272 Angle : 0.560 8.220 12815 Z= 0.282 Chirality : 0.039 0.155 1478 Planarity : 0.005 0.059 1344 Dihedral : 18.396 90.778 2232 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.06 % Allowed : 22.25 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.30), residues: 873 helix: 1.26 (0.30), residues: 307 sheet: -1.48 (0.42), residues: 168 loop : -0.71 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 82 HIS 0.004 0.001 HIS C 257 PHE 0.015 0.002 PHE A 139 TYR 0.019 0.002 TYR D 119 ARG 0.011 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6026 (mm) REVERT: A 71 MET cc_start: 0.6162 (mmm) cc_final: 0.5683 (mmm) REVERT: A 145 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: B 44 MET cc_start: 0.7550 (ttt) cc_final: 0.7313 (ttt) REVERT: B 435 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: C 272 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7219 (mt0) REVERT: D 85 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6675 (pm20) outliers start: 31 outliers final: 20 residues processed: 121 average time/residue: 0.2641 time to fit residues: 43.1015 Evaluate side-chains 119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9176 Z= 0.208 Angle : 0.527 8.264 12815 Z= 0.266 Chirality : 0.038 0.185 1478 Planarity : 0.004 0.048 1344 Dihedral : 18.409 92.234 2232 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.53 % Allowed : 23.95 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.30), residues: 873 helix: 1.32 (0.30), residues: 308 sheet: -1.40 (0.43), residues: 168 loop : -0.61 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 82 HIS 0.003 0.001 HIS C 257 PHE 0.014 0.001 PHE A 139 TYR 0.028 0.002 TYR D 119 ARG 0.008 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6051 (mm) REVERT: A 71 MET cc_start: 0.6018 (mmm) cc_final: 0.5616 (mmm) REVERT: A 145 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: B 44 MET cc_start: 0.7508 (ttt) cc_final: 0.7256 (ttt) REVERT: B 435 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: C 45 ARG cc_start: 0.7562 (ttt180) cc_final: 0.7278 (mtt-85) REVERT: C 272 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7194 (mm-40) REVERT: D 85 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: D 172 GLN cc_start: 0.7364 (mm-40) cc_final: 0.7158 (tt0) outliers start: 27 outliers final: 16 residues processed: 117 average time/residue: 0.2385 time to fit residues: 37.6923 Evaluate side-chains 112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 0.0070 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9176 Z= 0.159 Angle : 0.502 7.893 12815 Z= 0.254 Chirality : 0.037 0.156 1478 Planarity : 0.004 0.046 1344 Dihedral : 18.382 93.682 2232 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.40 % Allowed : 24.48 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.30), residues: 873 helix: 1.45 (0.30), residues: 311 sheet: -1.39 (0.44), residues: 160 loop : -0.51 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 82 HIS 0.003 0.001 HIS C 255 PHE 0.012 0.001 PHE A 139 TYR 0.019 0.002 TYR D 119 ARG 0.007 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5931 (mm) REVERT: A 49 MET cc_start: 0.5826 (mmm) cc_final: 0.5535 (mmt) REVERT: A 71 MET cc_start: 0.5957 (mmm) cc_final: 0.5530 (mmm) REVERT: A 145 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: B 11 ARG cc_start: 0.6270 (ttm110) cc_final: 0.5879 (tpp-160) REVERT: B 44 MET cc_start: 0.7462 (ttt) cc_final: 0.7177 (ttt) REVERT: B 380 TYR cc_start: 0.6984 (m-80) cc_final: 0.6691 (m-80) REVERT: B 435 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6354 (mp0) REVERT: C 45 ARG cc_start: 0.7352 (ttt180) cc_final: 0.7096 (mtt-85) REVERT: C 272 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7109 (mt0) REVERT: D 85 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6743 (pm20) outliers start: 26 outliers final: 14 residues processed: 119 average time/residue: 0.2398 time to fit residues: 38.6413 Evaluate side-chains 108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.0170 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 0.0470 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9176 Z= 0.150 Angle : 0.507 8.366 12815 Z= 0.254 Chirality : 0.037 0.211 1478 Planarity : 0.004 0.060 1344 Dihedral : 18.359 93.034 2232 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.01 % Allowed : 25.13 % Favored : 71.86 % 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: 0.06 (0.30), residues: 873 helix: 1.55 (0.30), residues: 310 sheet: -1.38 (0.44), residues: 159 loop : -0.47 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 82 HIS 0.003 0.001 HIS B 347 PHE 0.011 0.001 PHE A 139 TYR 0.020 0.002 TYR B 343 ARG 0.008 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5962 (mm) REVERT: A 49 MET cc_start: 0.5766 (mmm) cc_final: 0.5534 (mmt) REVERT: A 71 MET cc_start: 0.5967 (mmm) cc_final: 0.5530 (mmm) REVERT: A 145 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: B 11 ARG cc_start: 0.6242 (ttm110) cc_final: 0.5873 (tpp-160) REVERT: B 435 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: C 45 ARG cc_start: 0.7313 (ttt180) cc_final: 0.7036 (mtt-85) REVERT: C 272 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7108 (mt0) REVERT: D 85 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6775 (pm20) outliers start: 23 outliers final: 14 residues processed: 106 average time/residue: 0.2231 time to fit residues: 33.2673 Evaluate side-chains 104 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 504 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9176 Z= 0.174 Angle : 0.504 7.852 12815 Z= 0.255 Chirality : 0.037 0.242 1478 Planarity : 0.004 0.050 1344 Dihedral : 18.340 91.876 2232 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.75 % Allowed : 25.39 % Favored : 71.86 % 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: 0.13 (0.30), residues: 873 helix: 1.57 (0.30), residues: 310 sheet: -1.28 (0.44), residues: 159 loop : -0.42 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 82 HIS 0.004 0.001 HIS B 347 PHE 0.012 0.001 PHE A 139 TYR 0.023 0.002 TYR B 343 ARG 0.008 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5862 (mm) REVERT: A 49 MET cc_start: 0.5659 (mmm) cc_final: 0.5447 (mmt) REVERT: A 71 MET cc_start: 0.5862 (mmm) cc_final: 0.5452 (mmm) REVERT: A 145 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 160 MET cc_start: 0.7163 (mmp) cc_final: 0.6929 (mmm) REVERT: B 11 ARG cc_start: 0.6235 (ttm110) cc_final: 0.5856 (tpp-160) REVERT: B 396 ARG cc_start: 0.8022 (ttt-90) cc_final: 0.7808 (ttp80) REVERT: B 435 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: C 45 ARG cc_start: 0.7353 (ttt180) cc_final: 0.7062 (mtt-85) REVERT: D 85 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6761 (pm20) outliers start: 21 outliers final: 15 residues processed: 103 average time/residue: 0.2111 time to fit residues: 30.5039 Evaluate side-chains 101 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9176 Z= 0.246 Angle : 0.546 8.258 12815 Z= 0.275 Chirality : 0.039 0.289 1478 Planarity : 0.005 0.052 1344 Dihedral : 18.366 90.998 2232 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.75 % Allowed : 25.39 % Favored : 71.86 % 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: 0.04 (0.30), residues: 873 helix: 1.48 (0.30), residues: 309 sheet: -1.33 (0.44), residues: 160 loop : -0.45 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 82 HIS 0.003 0.001 HIS B 347 PHE 0.013 0.002 PHE A 139 TYR 0.024 0.002 TYR D 119 ARG 0.009 0.000 ARG C 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5823 (mm) REVERT: A 71 MET cc_start: 0.5888 (mmm) cc_final: 0.5457 (mmm) REVERT: A 145 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: B 11 ARG cc_start: 0.6268 (ttm110) cc_final: 0.5871 (tpp-160) REVERT: B 390 HIS cc_start: 0.7249 (m90) cc_final: 0.6822 (m170) REVERT: B 396 ARG cc_start: 0.8079 (ttt-90) cc_final: 0.7873 (ttp80) REVERT: B 435 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: D 85 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6707 (pm20) outliers start: 21 outliers final: 17 residues processed: 100 average time/residue: 0.2225 time to fit residues: 31.1397 Evaluate side-chains 101 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 0.0570 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.191062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155239 restraints weight = 9921.804| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.87 r_work: 0.3673 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9176 Z= 0.168 Angle : 0.510 7.668 12815 Z= 0.257 Chirality : 0.038 0.230 1478 Planarity : 0.004 0.044 1344 Dihedral : 18.368 93.087 2232 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.75 % Allowed : 25.39 % Favored : 71.86 % 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: 0.15 (0.30), residues: 873 helix: 1.61 (0.30), residues: 309 sheet: -1.33 (0.44), residues: 159 loop : -0.39 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 82 HIS 0.003 0.001 HIS B 347 PHE 0.012 0.001 PHE A 139 TYR 0.022 0.002 TYR D 119 ARG 0.009 0.000 ARG C 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1911.72 seconds wall clock time: 35 minutes 48.70 seconds (2148.70 seconds total)