Starting phenix.real_space_refine on Thu Mar 13 13:26:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iss_35694/03_2025/8iss_35694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iss_35694/03_2025/8iss_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/cci-nas-00/data/ceres_data/8iss_35694/03_2025/8iss_35694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iss_35694/03_2025/8iss_35694.map" model { file = "/net/cci-nas-00/data/ceres_data/8iss_35694/03_2025/8iss_35694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iss_35694/03_2025/8iss_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-5624/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: 5.27, per 1000 atoms: 0.60 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: 2.20 Conformation dependent library (CDL) restraints added in 791.4 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: 2.99 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: 2.83 Time building geometry restraints manager: 2.61 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: 0.580 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: 0.060 Set scattering table: 0.080 Process input model: 24.150 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- 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 : 0.855 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: 0.2836 time to fit residues: 37.7585 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 : 0.751 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.167871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131546 restraints weight = 9760.380| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.92 r_work: 0.3376 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 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 : 1.211 Fit side-chains REVERT: A 47 LEU cc_start: 0.6120 (mm) cc_final: 0.5910 (mm) REVERT: A 49 MET cc_start: 0.5739 (mpp) cc_final: 0.5246 (mpp) REVERT: A 71 MET cc_start: 0.6190 (mmm) cc_final: 0.5474 (mmm) REVERT: A 145 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: B 11 ARG cc_start: 0.6060 (ttm110) cc_final: 0.5505 (mtp85) REVERT: B 380 TYR cc_start: 0.6738 (m-80) cc_final: 0.6515 (m-80) REVERT: C 45 ARG cc_start: 0.7801 (ttt180) cc_final: 0.7498 (mtt-85) REVERT: C 103 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.5018 (mp0) REVERT: C 272 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6943 (mt0) REVERT: D 22 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7691 (mt-10) REVERT: D 85 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6445 (pm20) REVERT: D 497 ASP cc_start: 0.7646 (m-30) cc_final: 0.7423 (t0) outliers start: 23 outliers final: 6 residues processed: 123 average time/residue: 0.3848 time to fit residues: 64.4825 Evaluate side-chains 96 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 91 optimal weight: 6.9990 chunk 58 optimal weight: 0.0970 chunk 18 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.184082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148537 restraints weight = 9747.081| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.96 r_work: 0.3399 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9176 Z= 0.143 Angle : 0.498 6.211 12815 Z= 0.254 Chirality : 0.037 0.147 1478 Planarity : 0.004 0.044 1344 Dihedral : 18.260 91.061 2232 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.62 % Allowed : 20.81 % Favored : 76.57 % 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: -0.28 (0.29), residues: 873 helix: 1.46 (0.31), residues: 308 sheet: -1.56 (0.42), residues: 158 loop : -0.84 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 329 HIS 0.003 0.001 HIS B 347 PHE 0.012 0.001 PHE A 139 TYR 0.014 0.002 TYR B 343 ARG 0.007 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: 20 poor density : 103 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5917 (mm) cc_final: 0.5553 (mm) REVERT: A 71 MET cc_start: 0.6058 (mmm) cc_final: 0.5380 (mmm) REVERT: B 11 ARG cc_start: 0.5992 (ttm110) cc_final: 0.5460 (mtp85) REVERT: B 380 TYR cc_start: 0.6789 (m-80) cc_final: 0.6569 (m-80) REVERT: C 45 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7424 (mtt-85) REVERT: C 272 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6934 (mm-40) REVERT: D 85 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6530 (pm20) outliers start: 20 outliers final: 8 residues processed: 119 average time/residue: 0.2605 time to fit residues: 40.8202 Evaluate side-chains 100 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR 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 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 32 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 47 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.177936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141425 restraints weight = 9730.529| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.98 r_work: 0.3391 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1955 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= 0.211 Angle : 0.525 6.455 12815 Z= 0.265 Chirality : 0.038 0.139 1478 Planarity : 0.004 0.040 1344 Dihedral : 18.284 90.464 2232 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.14 % Allowed : 20.81 % 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: -0.23 (0.30), residues: 873 helix: 1.42 (0.30), residues: 308 sheet: -1.55 (0.42), residues: 162 loop : -0.72 (0.32), residues: 403 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 D 512 TYR 0.019 0.002 TYR B 343 ARG 0.008 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 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5965 (OUTLIER) cc_final: 0.5596 (mm) REVERT: A 71 MET cc_start: 0.5952 (mmm) cc_final: 0.5318 (mmm) REVERT: B 435 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: D 85 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6616 (pm20) REVERT: D 172 GLN cc_start: 0.7296 (mm-40) cc_final: 0.6753 (tt0) outliers start: 24 outliers final: 13 residues processed: 117 average time/residue: 0.2429 time to fit residues: 38.1785 Evaluate side-chains 110 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 72 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.178070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141492 restraints weight = 9765.827| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.99 r_work: 0.3452 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2058 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= 0.236 Angle : 0.538 6.445 12815 Z= 0.271 Chirality : 0.038 0.175 1478 Planarity : 0.004 0.051 1344 Dihedral : 18.343 90.798 2232 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.53 % Allowed : 22.25 % Favored : 74.21 % 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: 1.38 (0.30), residues: 307 sheet: -1.53 (0.43), residues: 161 loop : -0.63 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 82 HIS 0.004 0.001 HIS C 257 PHE 0.014 0.002 PHE A 139 TYR 0.021 0.002 TYR B 343 ARG 0.010 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 123 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5572 (mm) REVERT: A 71 MET cc_start: 0.5943 (mmm) cc_final: 0.5323 (mmm) REVERT: B 435 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: C 25 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7606 (mtm180) REVERT: C 45 ARG cc_start: 0.7778 (ttt180) cc_final: 0.7563 (ttt180) REVERT: D 85 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6634 (pm20) REVERT: D 172 GLN cc_start: 0.7483 (mm-40) cc_final: 0.6950 (tt0) outliers start: 27 outliers final: 18 residues processed: 115 average time/residue: 0.2434 time to fit residues: 37.3140 Evaluate side-chains 115 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 324 THR 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 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 504 LEU 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 80 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127046 restraints weight = 9854.888| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.91 r_work: 0.3448 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9176 Z= 0.230 Angle : 0.534 6.453 12815 Z= 0.269 Chirality : 0.038 0.176 1478 Planarity : 0.004 0.045 1344 Dihedral : 18.368 91.619 2232 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.66 % Allowed : 23.43 % Favored : 72.91 % 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: -0.17 (0.30), residues: 873 helix: 1.38 (0.30), residues: 308 sheet: -1.50 (0.44), residues: 161 loop : -0.61 (0.32), residues: 404 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 0.002 PHE A 139 TYR 0.020 0.002 TYR D 119 ARG 0.012 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 122 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5472 (mm) REVERT: A 49 MET cc_start: 0.5170 (mmm) cc_final: 0.4918 (mmt) REVERT: A 71 MET cc_start: 0.5958 (mmm) cc_final: 0.5369 (mmm) REVERT: B 435 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: C 25 ARG cc_start: 0.7863 (mtp180) cc_final: 0.7582 (mtm180) REVERT: C 45 ARG cc_start: 0.7789 (ttt180) cc_final: 0.7502 (mtt-85) REVERT: D 85 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6611 (pm20) REVERT: D 172 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7040 (tt0) outliers start: 28 outliers final: 17 residues processed: 115 average time/residue: 0.2457 time to fit residues: 37.7174 Evaluate side-chains 107 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER 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 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 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 504 LEU 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 79 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.191136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156599 restraints weight = 10081.911| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.80 r_work: 0.3670 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9176 Z= 0.182 Angle : 0.507 6.554 12815 Z= 0.257 Chirality : 0.037 0.135 1478 Planarity : 0.005 0.060 1344 Dihedral : 18.370 93.039 2232 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.40 % Allowed : 23.95 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.30), residues: 873 helix: 1.52 (0.30), residues: 309 sheet: -1.36 (0.44), residues: 159 loop : -0.52 (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 0.026 0.002 TYR D 119 ARG 0.012 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 116 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5864 (mm) REVERT: A 49 MET cc_start: 0.5851 (mmm) cc_final: 0.5597 (mmt) REVERT: A 71 MET cc_start: 0.6188 (mmm) cc_final: 0.5666 (mmm) REVERT: B 380 TYR cc_start: 0.6847 (m-80) cc_final: 0.6618 (m-80) REVERT: B 435 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: C 25 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7779 (mtm180) REVERT: C 45 ARG cc_start: 0.7735 (ttt180) cc_final: 0.7529 (mtt-85) REVERT: C 272 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7249 (mt0) REVERT: D 85 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6810 (pm20) REVERT: D 172 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7254 (tt0) outliers start: 26 outliers final: 16 residues processed: 112 average time/residue: 0.2434 time to fit residues: 36.9094 Evaluate side-chains 105 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU 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 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 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 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 504 LEU 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 77 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.190822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155004 restraints weight = 10065.929| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.87 r_work: 0.3687 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9176 Z= 0.170 Angle : 0.497 6.432 12815 Z= 0.251 Chirality : 0.037 0.136 1478 Planarity : 0.004 0.050 1344 Dihedral : 18.349 92.821 2232 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.01 % Allowed : 23.95 % Favored : 73.04 % 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: 0.08 (0.30), residues: 873 helix: 1.56 (0.30), residues: 309 sheet: -1.30 (0.44), residues: 159 loop : -0.47 (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 C 255 PHE 0.012 0.001 PHE A 139 TYR 0.021 0.002 TYR B 343 ARG 0.013 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 : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5909 (mm) REVERT: A 71 MET cc_start: 0.6152 (mmm) cc_final: 0.5653 (mmm) REVERT: B 11 ARG cc_start: 0.6268 (ttm110) cc_final: 0.5893 (tpp-160) REVERT: B 380 TYR cc_start: 0.6819 (m-80) cc_final: 0.6567 (m-80) REVERT: B 435 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: C 25 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7726 (mtm180) REVERT: C 45 ARG cc_start: 0.7640 (ttt180) cc_final: 0.7411 (mtt-85) REVERT: C 272 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7195 (mt0) REVERT: D 85 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6812 (pm20) REVERT: D 172 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7234 (tt0) outliers start: 23 outliers final: 16 residues processed: 107 average time/residue: 0.2320 time to fit residues: 33.8420 Evaluate side-chains 104 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER 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 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 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 504 LEU Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.190959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155015 restraints weight = 9996.025| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.87 r_work: 0.3696 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9176 Z= 0.166 Angle : 0.499 6.434 12815 Z= 0.252 Chirality : 0.037 0.135 1478 Planarity : 0.004 0.055 1344 Dihedral : 18.340 92.587 2232 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.62 % Allowed : 24.21 % Favored : 73.17 % 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: -1.27 (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 0.003 0.001 HIS B 347 PHE 0.011 0.001 PHE A 139 TYR 0.030 0.002 TYR B 348 ARG 0.014 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 108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5848 (mm) REVERT: A 71 MET cc_start: 0.6071 (mmm) cc_final: 0.5599 (mmm) REVERT: B 11 ARG cc_start: 0.6294 (ttm110) cc_final: 0.5909 (tpp-160) REVERT: B 380 TYR cc_start: 0.6834 (m-80) cc_final: 0.6597 (m-80) REVERT: B 435 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6481 (mp0) REVERT: C 25 ARG cc_start: 0.7983 (mtp180) cc_final: 0.7753 (mtm180) REVERT: C 272 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7154 (mt0) REVERT: D 85 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6832 (pm20) REVERT: D 172 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7286 (tt0) outliers start: 20 outliers final: 15 residues processed: 105 average time/residue: 0.2438 time to fit residues: 35.2731 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 : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU 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 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 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 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: 2.9990 chunk 2 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 0.0370 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 76 optimal weight: 0.0060 overall best weight: 0.5074 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.193269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158013 restraints weight = 9954.646| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.85 r_work: 0.3734 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9176 Z= 0.146 Angle : 0.488 6.426 12815 Z= 0.246 Chirality : 0.036 0.135 1478 Planarity : 0.005 0.058 1344 Dihedral : 18.328 92.631 2232 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.49 % Allowed : 24.21 % Favored : 73.30 % 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: 0.21 (0.30), residues: 873 helix: 1.63 (0.30), residues: 310 sheet: -1.25 (0.45), residues: 159 loop : -0.37 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 82 HIS 0.003 0.000 HIS B 347 PHE 0.012 0.001 PHE A 139 TYR 0.022 0.002 TYR B 348 ARG 0.015 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 104 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5769 (mm) REVERT: A 71 MET cc_start: 0.6049 (mmm) cc_final: 0.5608 (mmm) REVERT: B 11 ARG cc_start: 0.6261 (ttm110) cc_final: 0.5892 (tpp-160) REVERT: B 380 TYR cc_start: 0.6725 (m-80) cc_final: 0.6501 (m-80) REVERT: B 390 HIS cc_start: 0.7443 (m90) cc_final: 0.7056 (m170) REVERT: B 435 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: C 25 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7794 (mtm180) REVERT: D 85 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6868 (pm20) REVERT: D 172 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7279 (tt0) outliers start: 19 outliers final: 16 residues processed: 100 average time/residue: 0.2314 time to fit residues: 31.9312 Evaluate side-chains 102 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER 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 D residue 74 LEU 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 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 44 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 0.1980 chunk 66 optimal weight: 0.0980 chunk 60 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN D 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.193925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158728 restraints weight = 10044.973| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.86 r_work: 0.3730 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9176 Z= 0.144 Angle : 0.483 6.440 12815 Z= 0.243 Chirality : 0.036 0.133 1478 Planarity : 0.004 0.056 1344 Dihedral : 18.308 91.902 2232 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.75 % Allowed : 24.35 % Favored : 72.91 % 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: 0.28 (0.30), residues: 873 helix: 1.68 (0.30), residues: 310 sheet: -1.20 (0.45), residues: 157 loop : -0.33 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 82 HIS 0.003 0.001 HIS B 347 PHE 0.012 0.001 PHE A 139 TYR 0.021 0.002 TYR D 119 ARG 0.015 0.000 ARG C 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4930.88 seconds wall clock time: 87 minutes 38.65 seconds (5258.65 seconds total)