Starting phenix.real_space_refine on Tue Feb 11 08:27:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u2k_20621/02_2025/6u2k_20621_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u2k_20621/02_2025/6u2k_20621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u2k_20621/02_2025/6u2k_20621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u2k_20621/02_2025/6u2k_20621.map" model { file = "/net/cci-nas-00/data/ceres_data/6u2k_20621/02_2025/6u2k_20621_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u2k_20621/02_2025/6u2k_20621_neut.cif" } resolution = 2.93 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 ------------------------------------------------------------------------------- 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= 0.031 sd= 0.579 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2979 2.51 5 N 802 2.21 5 O 912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4719 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 4663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4663 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 569} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.14, per 1000 atoms: 0.67 Number of scatterers: 4719 At special positions: 0 Unit cell: (96.46, 75.26, 104.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 912 8.00 N 802 7.00 C 2979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 368 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 395 " - pdb=" SG CYS B 438 " distance=2.03 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 545 " distance=2.02 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 1 " - " ASN B 168 " " NAG C 1 " - " ASN B 252 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 593.5 milliseconds 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 11 sheets defined 19.0% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 removed outlier: 4.047A pdb=" N CYS B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.619A pdb=" N THR B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.583A pdb=" N THR B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.656A pdb=" N LYS B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.726A pdb=" N VAL B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.994A pdb=" N GLN B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 211' Processing helix chain 'B' and resid 215 through 233 removed outlier: 3.719A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 294 through 297 removed outlier: 3.615A pdb=" N ILE B 297 " --> pdb=" O HIS B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 297' Processing helix chain 'B' and resid 309 through 327 removed outlier: 3.795A pdb=" N LYS B 315 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.535A pdb=" N MET B 42 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 40 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.858A pdb=" N ALA B 194 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR B 190 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR B 189 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 291 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 191 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP B 287 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY B 195 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA B 285 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.741A pdb=" N THR B 130 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 199 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 258 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU B 201 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B 256 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS B 203 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 368 Processing sheet with id=AA6, first strand: chain 'B' and resid 364 through 368 Processing sheet with id=AA7, first strand: chain 'B' and resid 411 through 414 removed outlier: 3.897A pdb=" N TYR B 413 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 427 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 417 through 418 Processing sheet with id=AA9, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AB1, first strand: chain 'B' and resid 501 through 505 removed outlier: 5.504A pdb=" N CYS B 545 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE B 504 " --> pdb=" O SER B 543 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER B 543 " --> pdb=" O PHE B 504 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 542 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 579 through 582 removed outlier: 3.561A pdb=" N ASN B 582 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG B 587 " --> pdb=" O ASN B 582 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 599 " --> pdb=" O ILE B 590 " (cutoff:3.500A) 110 hydrogen bonds defined for protein. 306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1497 1.34 - 1.46: 1046 1.46 - 1.58: 2244 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 4823 Sorted by residual: bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" CB ASN B 328 " pdb=" CG ASN B 328 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.93e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" CB VAL B 310 " pdb=" CG1 VAL B 310 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.63e+00 bond pdb=" CB VAL B 142 " pdb=" CG1 VAL B 142 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.47e+00 ... (remaining 4818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 6084 1.74 - 3.48: 402 3.48 - 5.22: 53 5.22 - 6.96: 10 6.96 - 8.70: 7 Bond angle restraints: 6556 Sorted by residual: angle pdb=" CA TYR B 50 " pdb=" CB TYR B 50 " pdb=" CG TYR B 50 " ideal model delta sigma weight residual 113.90 122.23 -8.33 1.80e+00 3.09e-01 2.14e+01 angle pdb=" C HIS B 403 " pdb=" N LEU B 404 " pdb=" CA LEU B 404 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C ARG B 375 " pdb=" N ASP B 376 " pdb=" CA ASP B 376 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C PHE B 480 " pdb=" N GLU B 481 " pdb=" CA GLU B 481 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N PHE B 327 " pdb=" CA PHE B 327 " pdb=" C PHE B 327 " ideal model delta sigma weight residual 110.53 105.83 4.70 1.32e+00 5.74e-01 1.27e+01 ... (remaining 6551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 2789 14.88 - 29.76: 126 29.76 - 44.64: 36 44.64 - 59.52: 9 59.52 - 74.40: 4 Dihedral angle restraints: 2964 sinusoidal: 1218 harmonic: 1746 Sorted by residual: dihedral pdb=" CA VAL B 402 " pdb=" C VAL B 402 " pdb=" N HIS B 403 " pdb=" CA HIS B 403 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA VAL B 135 " pdb=" C VAL B 135 " pdb=" N ARG B 136 " pdb=" CA ARG B 136 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO B 396 " pdb=" C PRO B 396 " pdb=" N SER B 397 " pdb=" CA SER B 397 " ideal model delta harmonic sigma weight residual 180.00 -156.87 -23.13 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 2961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 379 0.042 - 0.083: 246 0.083 - 0.125: 87 0.125 - 0.166: 30 0.166 - 0.208: 7 Chirality restraints: 749 Sorted by residual: chirality pdb=" CB ILE B 579 " pdb=" CA ILE B 579 " pdb=" CG1 ILE B 579 " pdb=" CG2 ILE B 579 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE B 67 " pdb=" N ILE B 67 " pdb=" C ILE B 67 " pdb=" CB ILE B 67 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CB THR B 552 " pdb=" CA THR B 552 " pdb=" OG1 THR B 552 " pdb=" CG2 THR B 552 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 746 not shown) Planarity restraints: 855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 404 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU B 404 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU B 404 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 405 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 330 " 0.051 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO B 331 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 480 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C PHE B 480 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE B 480 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU B 481 " 0.014 2.00e-02 2.50e+03 ... (remaining 852 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1667 2.86 - 3.37: 3987 3.37 - 3.88: 7168 3.88 - 4.39: 8323 4.39 - 4.90: 14511 Nonbonded interactions: 35656 Sorted by model distance: nonbonded pdb=" OG SER B 248 " pdb=" OD1 ASN B 252 " model vdw 2.354 3.040 nonbonded pdb=" ND2 ASN B 387 " pdb=" O SER B 394 " model vdw 2.359 3.120 nonbonded pdb=" O TYR B 325 " pdb=" OG1 THR B 329 " model vdw 2.387 3.040 nonbonded pdb=" O CYS B 507 " pdb=" NZ LYS B 523 " model vdw 2.397 3.120 nonbonded pdb=" ND2 ASN B 414 " pdb=" O HIS B 415 " model vdw 2.428 3.120 ... (remaining 35651 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.940 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.010 0.074 4823 Z= 0.658 Angle : 0.989 8.704 6556 Z= 0.542 Chirality : 0.061 0.208 749 Planarity : 0.008 0.078 853 Dihedral : 10.371 74.405 1814 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 0.19 % Allowed : 4.44 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -4.70 (0.27), residues: 598 helix: -4.66 (0.16), residues: 119 sheet: -2.91 (0.40), residues: 113 loop : -2.72 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 437 HIS 0.009 0.002 HIS B 203 PHE 0.032 0.004 PHE B 551 TYR 0.031 0.004 TYR B 324 ARG 0.013 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ASP cc_start: 0.8434 (t0) cc_final: 0.7643 (t0) REVERT: B 127 GLN cc_start: 0.7974 (mt0) cc_final: 0.7601 (mt0) REVERT: B 251 SER cc_start: 0.9010 (m) cc_final: 0.8808 (t) REVERT: B 289 SER cc_start: 0.8838 (t) cc_final: 0.8615 (p) REVERT: B 423 GLU cc_start: 0.8517 (pp20) cc_final: 0.7196 (tt0) REVERT: B 434 ARG cc_start: 0.8202 (mpp80) cc_final: 0.7974 (mtm180) REVERT: B 482 ASN cc_start: 0.8200 (m110) cc_final: 0.7947 (m-40) REVERT: B 488 SER cc_start: 0.8478 (t) cc_final: 0.8276 (p) REVERT: B 576 ASN cc_start: 0.7527 (t0) cc_final: 0.7307 (t0) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.9052 time to fit residues: 132.8995 Evaluate side-chains 100 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 0.0010 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 52 ASN B 80 ASN B 109 ASN B 255 ASN B 370 GLN B 387 ASN B 414 ASN B 489 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106951 restraints weight = 5690.045| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.75 r_work: 0.3139 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4823 Z= 0.172 Angle : 0.613 6.517 6556 Z= 0.328 Chirality : 0.045 0.190 749 Planarity : 0.006 0.042 853 Dihedral : 7.240 56.108 727 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.09 % Allowed : 11.58 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.86 (0.29), residues: 598 helix: -3.24 (0.34), residues: 119 sheet: -2.81 (0.39), residues: 125 loop : -2.24 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 275 HIS 0.002 0.001 HIS B 282 PHE 0.015 0.002 PHE B 68 TYR 0.015 0.002 TYR B 50 ARG 0.004 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 14 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 79 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8450 (mmm) REVERT: B 127 GLN cc_start: 0.7844 (mt0) cc_final: 0.7332 (mt0) REVERT: B 289 SER cc_start: 0.9134 (t) cc_final: 0.8707 (p) REVERT: B 333 CYS cc_start: 0.7936 (t) cc_final: 0.7482 (t) REVERT: B 381 GLN cc_start: 0.8603 (tt0) cc_final: 0.8172 (pt0) REVERT: B 411 GLU cc_start: 0.8396 (tp30) cc_final: 0.8058 (tt0) REVERT: B 423 GLU cc_start: 0.7842 (pp20) cc_final: 0.6924 (tp30) REVERT: B 460 SER cc_start: 0.8532 (t) cc_final: 0.8204 (p) REVERT: B 481 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8057 (pt0) REVERT: B 482 ASN cc_start: 0.8297 (m110) cc_final: 0.7915 (m-40) REVERT: B 488 SER cc_start: 0.8216 (t) cc_final: 0.7951 (p) outliers start: 16 outliers final: 8 residues processed: 110 average time/residue: 0.8451 time to fit residues: 98.0683 Evaluate side-chains 104 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 579 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.144479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108932 restraints weight = 5784.664| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.80 r_work: 0.3126 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4823 Z= 0.188 Angle : 0.564 7.344 6556 Z= 0.302 Chirality : 0.044 0.157 749 Planarity : 0.005 0.034 853 Dihedral : 6.324 55.341 727 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.51 % Allowed : 14.86 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.26 (0.30), residues: 598 helix: -2.03 (0.43), residues: 118 sheet: -2.57 (0.39), residues: 126 loop : -2.08 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 437 HIS 0.002 0.001 HIS B 203 PHE 0.013 0.001 PHE B 480 TYR 0.011 0.001 TYR B 324 ARG 0.003 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4416 (tt0) cc_final: 0.4159 (tt0) REVERT: B 79 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8500 (mmm) REVERT: B 127 GLN cc_start: 0.7910 (mt0) cc_final: 0.7595 (mt0) REVERT: B 172 MET cc_start: 0.8416 (tpt) cc_final: 0.8039 (tpt) REVERT: B 251 SER cc_start: 0.8718 (m) cc_final: 0.8350 (t) REVERT: B 289 SER cc_start: 0.9092 (t) cc_final: 0.8636 (p) REVERT: B 381 GLN cc_start: 0.8546 (tt0) cc_final: 0.8152 (pt0) REVERT: B 411 GLU cc_start: 0.8457 (tp30) cc_final: 0.8089 (tt0) REVERT: B 423 GLU cc_start: 0.7726 (pp20) cc_final: 0.7008 (tp30) REVERT: B 460 SER cc_start: 0.8451 (t) cc_final: 0.8175 (p) REVERT: B 488 SER cc_start: 0.8172 (t) cc_final: 0.7943 (p) outliers start: 13 outliers final: 7 residues processed: 106 average time/residue: 0.8512 time to fit residues: 95.0458 Evaluate side-chains 99 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 579 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107294 restraints weight = 5843.942| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.79 r_work: 0.3110 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 4823 Z= 0.270 Angle : 0.606 9.065 6556 Z= 0.320 Chirality : 0.045 0.190 749 Planarity : 0.005 0.036 853 Dihedral : 6.141 55.636 727 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.09 % Allowed : 16.22 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.02 (0.31), residues: 598 helix: -1.75 (0.44), residues: 124 sheet: -2.41 (0.40), residues: 126 loop : -1.94 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 437 HIS 0.003 0.001 HIS B 203 PHE 0.017 0.002 PHE B 497 TYR 0.014 0.001 TYR B 324 ARG 0.004 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ASN cc_start: 0.7925 (m-40) cc_final: 0.7643 (m110) REVERT: B 57 GLU cc_start: 0.4096 (tt0) cc_final: 0.3492 (tt0) REVERT: B 127 GLN cc_start: 0.7758 (mt0) cc_final: 0.7457 (mt0) REVERT: B 251 SER cc_start: 0.8675 (m) cc_final: 0.8309 (t) REVERT: B 289 SER cc_start: 0.9073 (t) cc_final: 0.8618 (p) REVERT: B 381 GLN cc_start: 0.8550 (tt0) cc_final: 0.8230 (pt0) REVERT: B 411 GLU cc_start: 0.8463 (tp30) cc_final: 0.8115 (tt0) REVERT: B 423 GLU cc_start: 0.7657 (pp20) cc_final: 0.6975 (tp30) REVERT: B 460 SER cc_start: 0.8383 (t) cc_final: 0.8081 (p) REVERT: B 464 MET cc_start: 0.8823 (mmm) cc_final: 0.8622 (mmp) REVERT: B 488 SER cc_start: 0.8182 (t) cc_final: 0.7899 (p) outliers start: 16 outliers final: 6 residues processed: 100 average time/residue: 0.8618 time to fit residues: 90.8490 Evaluate side-chains 95 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 579 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107896 restraints weight = 5923.367| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.79 r_work: 0.3104 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4823 Z= 0.237 Angle : 0.586 7.760 6556 Z= 0.311 Chirality : 0.046 0.167 749 Planarity : 0.004 0.032 853 Dihedral : 5.995 55.197 727 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.09 % Allowed : 16.80 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.32), residues: 598 helix: -1.34 (0.46), residues: 124 sheet: -2.27 (0.40), residues: 125 loop : -1.84 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 87 HIS 0.003 0.001 HIS B 203 PHE 0.013 0.002 PHE B 68 TYR 0.013 0.001 TYR B 324 ARG 0.003 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 ASN cc_start: 0.7430 (m-40) cc_final: 0.7153 (m110) REVERT: B 57 GLU cc_start: 0.4171 (tt0) cc_final: 0.3493 (tt0) REVERT: B 127 GLN cc_start: 0.7647 (mt0) cc_final: 0.7377 (mt0) REVERT: B 156 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7655 (tmtt) REVERT: B 289 SER cc_start: 0.9047 (t) cc_final: 0.8644 (m) REVERT: B 381 GLN cc_start: 0.8556 (tt0) cc_final: 0.8206 (pt0) REVERT: B 411 GLU cc_start: 0.8480 (tp30) cc_final: 0.8146 (tt0) REVERT: B 423 GLU cc_start: 0.7653 (pp20) cc_final: 0.6976 (tp30) REVERT: B 460 SER cc_start: 0.8380 (t) cc_final: 0.8078 (p) REVERT: B 488 SER cc_start: 0.8144 (t) cc_final: 0.7876 (p) outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 0.8541 time to fit residues: 89.4067 Evaluate side-chains 99 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 587 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 15 optimal weight: 0.0040 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110705 restraints weight = 5830.836| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.80 r_work: 0.3142 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4823 Z= 0.171 Angle : 0.562 7.062 6556 Z= 0.295 Chirality : 0.044 0.161 749 Planarity : 0.004 0.033 853 Dihedral : 5.883 52.368 727 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.70 % Allowed : 17.18 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.32), residues: 598 helix: -1.07 (0.45), residues: 130 sheet: -2.14 (0.40), residues: 116 loop : -1.84 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 87 HIS 0.002 0.001 HIS B 203 PHE 0.011 0.001 PHE B 456 TYR 0.012 0.001 TYR B 50 ARG 0.003 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4316 (tt0) cc_final: 0.3633 (tt0) REVERT: B 127 GLN cc_start: 0.7604 (mt0) cc_final: 0.7322 (mt0) REVERT: B 156 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7631 (tmtt) REVERT: B 289 SER cc_start: 0.8843 (t) cc_final: 0.8434 (m) REVERT: B 381 GLN cc_start: 0.8458 (tt0) cc_final: 0.8174 (pt0) REVERT: B 411 GLU cc_start: 0.8221 (tp30) cc_final: 0.7872 (tt0) REVERT: B 460 SER cc_start: 0.8233 (t) cc_final: 0.7792 (p) REVERT: B 464 MET cc_start: 0.8731 (mmm) cc_final: 0.8434 (mmp) REVERT: B 488 SER cc_start: 0.7998 (t) cc_final: 0.7762 (p) REVERT: B 587 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6623 (mtm180) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.8574 time to fit residues: 89.6883 Evaluate side-chains 97 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 587 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 0.0170 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 0.0370 chunk 5 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 55 optimal weight: 0.3980 chunk 29 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS B 358 ASN B 489 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.147389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111628 restraints weight = 5844.711| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.79 r_work: 0.3172 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4823 Z= 0.158 Angle : 0.557 7.667 6556 Z= 0.291 Chirality : 0.044 0.158 749 Planarity : 0.004 0.033 853 Dihedral : 5.775 53.620 727 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.47 % Allowed : 17.95 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.32), residues: 598 helix: -0.76 (0.46), residues: 130 sheet: -2.10 (0.39), residues: 122 loop : -1.70 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 87 HIS 0.002 0.000 HIS B 203 PHE 0.011 0.001 PHE B 68 TYR 0.012 0.001 TYR B 50 ARG 0.003 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4358 (tt0) cc_final: 0.3530 (tt0) REVERT: B 126 ASP cc_start: 0.8596 (m-30) cc_final: 0.8327 (m-30) REVERT: B 127 GLN cc_start: 0.7601 (mt0) cc_final: 0.7309 (mt0) REVERT: B 129 ILE cc_start: 0.7765 (pt) cc_final: 0.7425 (pp) REVERT: B 156 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7647 (tmtt) REVERT: B 289 SER cc_start: 0.8796 (t) cc_final: 0.8382 (m) REVERT: B 381 GLN cc_start: 0.8376 (tt0) cc_final: 0.8091 (pt0) REVERT: B 411 GLU cc_start: 0.8226 (tp30) cc_final: 0.7893 (tt0) REVERT: B 424 ASP cc_start: 0.7952 (p0) cc_final: 0.7566 (p0) REVERT: B 460 SER cc_start: 0.8204 (t) cc_final: 0.7776 (p) REVERT: B 464 MET cc_start: 0.8706 (mmm) cc_final: 0.8421 (mmp) outliers start: 18 outliers final: 10 residues processed: 96 average time/residue: 0.7948 time to fit residues: 80.9956 Evaluate side-chains 93 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 579 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 44 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 489 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.147923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112017 restraints weight = 5858.141| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.80 r_work: 0.3176 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4823 Z= 0.176 Angle : 0.578 9.214 6556 Z= 0.298 Chirality : 0.044 0.156 749 Planarity : 0.004 0.033 853 Dihedral : 5.777 53.792 727 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.47 % Allowed : 18.92 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.33), residues: 598 helix: -0.56 (0.47), residues: 130 sheet: -2.06 (0.39), residues: 127 loop : -1.57 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 87 HIS 0.002 0.001 HIS B 415 PHE 0.011 0.001 PHE B 68 TYR 0.011 0.001 TYR B 50 ARG 0.003 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4287 (tt0) cc_final: 0.3387 (tt0) REVERT: B 127 GLN cc_start: 0.7574 (mt0) cc_final: 0.7296 (mt0) REVERT: B 156 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7595 (tmtt) REVERT: B 289 SER cc_start: 0.8822 (t) cc_final: 0.8402 (m) REVERT: B 381 GLN cc_start: 0.8340 (tt0) cc_final: 0.8073 (pt0) REVERT: B 411 GLU cc_start: 0.8223 (tp30) cc_final: 0.7903 (tt0) REVERT: B 464 MET cc_start: 0.8663 (mmm) cc_final: 0.8386 (mmp) REVERT: B 587 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6536 (mtm180) outliers start: 18 outliers final: 9 residues processed: 94 average time/residue: 0.9347 time to fit residues: 92.3820 Evaluate side-chains 95 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 587 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN B 489 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108788 restraints weight = 5855.011| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.78 r_work: 0.3133 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4823 Z= 0.257 Angle : 0.600 8.831 6556 Z= 0.312 Chirality : 0.046 0.151 749 Planarity : 0.004 0.032 853 Dihedral : 5.938 54.549 727 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.90 % Allowed : 20.27 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.33), residues: 598 helix: -0.44 (0.48), residues: 124 sheet: -2.16 (0.38), residues: 127 loop : -1.51 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 87 HIS 0.003 0.001 HIS B 282 PHE 0.013 0.002 PHE B 68 TYR 0.013 0.001 TYR B 324 ARG 0.003 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4382 (tt0) cc_final: 0.3306 (tt0) REVERT: B 126 ASP cc_start: 0.8628 (m-30) cc_final: 0.8348 (m-30) REVERT: B 127 GLN cc_start: 0.7565 (mt0) cc_final: 0.7280 (mt0) REVERT: B 129 ILE cc_start: 0.8058 (pt) cc_final: 0.7733 (pp) REVERT: B 289 SER cc_start: 0.8998 (t) cc_final: 0.8541 (p) REVERT: B 381 GLN cc_start: 0.8429 (tt0) cc_final: 0.8086 (pt0) REVERT: B 411 GLU cc_start: 0.8397 (tp30) cc_final: 0.8099 (tt0) REVERT: B 464 MET cc_start: 0.8813 (mmm) cc_final: 0.8532 (mmp) outliers start: 15 outliers final: 12 residues processed: 90 average time/residue: 0.9653 time to fit residues: 91.2219 Evaluate side-chains 95 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 579 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 chunk 10 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112177 restraints weight = 5859.393| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.80 r_work: 0.3181 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4823 Z= 0.167 Angle : 0.563 8.072 6556 Z= 0.289 Chirality : 0.044 0.164 749 Planarity : 0.004 0.033 853 Dihedral : 5.738 53.274 727 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.32 % Allowed : 20.46 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.98 (0.33), residues: 598 helix: -0.17 (0.50), residues: 125 sheet: -2.03 (0.39), residues: 127 loop : -1.45 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 87 HIS 0.002 0.001 HIS B 415 PHE 0.011 0.001 PHE B 497 TYR 0.010 0.001 TYR B 50 ARG 0.002 0.000 ARG B 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4368 (tt0) cc_final: 0.3407 (tt0) REVERT: B 126 ASP cc_start: 0.8500 (m-30) cc_final: 0.8107 (m-30) REVERT: B 127 GLN cc_start: 0.7516 (mt0) cc_final: 0.7238 (mt0) REVERT: B 129 ILE cc_start: 0.7876 (pt) cc_final: 0.7609 (pp) REVERT: B 156 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7594 (tmtt) REVERT: B 289 SER cc_start: 0.8810 (t) cc_final: 0.8296 (p) REVERT: B 381 GLN cc_start: 0.8281 (tt0) cc_final: 0.7980 (pt0) REVERT: B 411 GLU cc_start: 0.8145 (tp30) cc_final: 0.7795 (tt0) REVERT: B 587 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6546 (mtm180) outliers start: 12 outliers final: 11 residues processed: 89 average time/residue: 1.0343 time to fit residues: 96.3517 Evaluate side-chains 94 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 587 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 48 optimal weight: 0.0060 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.147335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111160 restraints weight = 5882.897| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.80 r_work: 0.3170 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4823 Z= 0.179 Angle : 0.566 8.326 6556 Z= 0.290 Chirality : 0.044 0.161 749 Planarity : 0.004 0.032 853 Dihedral : 5.689 53.803 727 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.93 % Allowed : 21.81 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.92 (0.33), residues: 598 helix: -0.04 (0.50), residues: 124 sheet: -2.02 (0.38), residues: 127 loop : -1.43 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 87 HIS 0.001 0.000 HIS B 282 PHE 0.011 0.001 PHE B 68 TYR 0.011 0.001 TYR B 50 ARG 0.002 0.000 ARG B 132 =============================================================================== Job complete usr+sys time: 3726.11 seconds wall clock time: 66 minutes 31.89 seconds (3991.89 seconds total)