Starting phenix.real_space_refine on Tue Mar 3 13:09:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u2k_20621/03_2026/6u2k_20621_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u2k_20621/03_2026/6u2k_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 { model { file = "/net/cci-nas-00/data/ceres_data/6u2k_20621/03_2026/6u2k_20621_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u2k_20621/03_2026/6u2k_20621_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u2k_20621/03_2026/6u2k_20621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u2k_20621/03_2026/6u2k_20621.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1, '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: 1.29, per 1000 atoms: 0.27 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: 0.41 Conformation dependent library (CDL) restraints added in 338.5 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: 0.16 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: 0.68 Time building geometry restraints manager: 0.52 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: 0.560 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.020 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- 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 4835 Z= 0.425 Angle : 0.995 8.704 6584 Z= 0.543 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 : 3.23 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.013 0.001 ARG B 132 TYR 0.031 0.004 TYR B 324 PHE 0.032 0.004 PHE B 551 TRP 0.022 0.003 TRP B 437 HIS 0.009 0.002 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.01007 ( 4823) covalent geometry : angle 0.98937 ( 6556) SS BOND : bond 0.00426 ( 8) SS BOND : angle 1.33140 ( 16) hydrogen bonds : bond 0.31965 ( 106) hydrogen bonds : angle 10.46826 ( 306) link_BETA1-4 : bond 0.00592 ( 2) link_BETA1-4 : angle 3.11337 ( 6) link_NAG-ASN : bond 0.00926 ( 2) link_NAG-ASN : angle 1.73996 ( 6) *********************** 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 : 0.214 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: 0.4541 time to fit residues: 66.4472 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 : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.0020 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 255 ASN B 370 GLN B 387 ASN B 414 ASN B 489 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106500 restraints weight = 5780.056| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.77 r_work: 0.3107 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4835 Z= 0.127 Angle : 0.623 6.540 6584 Z= 0.333 Chirality : 0.045 0.167 749 Planarity : 0.006 0.045 853 Dihedral : 7.229 55.924 727 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.29), residues: 598 helix: -3.29 (0.34), residues: 119 sheet: -2.84 (0.39), residues: 117 loop : -2.22 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 257 TYR 0.015 0.002 TYR B 50 PHE 0.014 0.002 PHE B 480 TRP 0.012 0.001 TRP B 275 HIS 0.002 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4823) covalent geometry : angle 0.61506 ( 6556) SS BOND : bond 0.00352 ( 8) SS BOND : angle 1.64886 ( 16) hydrogen bonds : bond 0.05076 ( 106) hydrogen bonds : angle 6.11816 ( 306) link_BETA1-4 : bond 0.00589 ( 2) link_BETA1-4 : angle 2.07927 ( 6) link_NAG-ASN : bond 0.01564 ( 2) link_NAG-ASN : angle 1.28827 ( 6) *********************** 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 119 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 14 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7686 (p) REVERT: B 79 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8478 (mmm) REVERT: B 127 GLN cc_start: 0.7848 (mt0) cc_final: 0.7335 (mt0) REVERT: B 289 SER cc_start: 0.9132 (t) cc_final: 0.8705 (p) REVERT: B 333 CYS cc_start: 0.7960 (t) cc_final: 0.7509 (t) REVERT: B 381 GLN cc_start: 0.8611 (tt0) cc_final: 0.8199 (pt0) REVERT: B 411 GLU cc_start: 0.8405 (tp30) cc_final: 0.8069 (tt0) REVERT: B 423 GLU cc_start: 0.7850 (pp20) cc_final: 0.6926 (tp30) REVERT: B 460 SER cc_start: 0.8532 (t) cc_final: 0.8208 (p) REVERT: B 482 ASN cc_start: 0.8308 (m110) cc_final: 0.7846 (m-40) REVERT: B 488 SER cc_start: 0.8234 (t) cc_final: 0.7968 (p) outliers start: 16 outliers final: 8 residues processed: 111 average time/residue: 0.3837 time to fit residues: 44.8379 Evaluate side-chains 105 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.143233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107561 restraints weight = 5766.334| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.78 r_work: 0.3105 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4835 Z= 0.146 Angle : 0.588 7.850 6584 Z= 0.313 Chirality : 0.045 0.159 749 Planarity : 0.005 0.034 853 Dihedral : 6.427 55.552 727 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.90 % Allowed : 14.67 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.30), residues: 598 helix: -2.10 (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 ARG 0.003 0.000 ARG B 257 TYR 0.013 0.001 TYR B 324 PHE 0.015 0.002 PHE B 480 TRP 0.010 0.001 TRP B 437 HIS 0.003 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4823) covalent geometry : angle 0.58011 ( 6556) SS BOND : bond 0.00272 ( 8) SS BOND : angle 1.70148 ( 16) hydrogen bonds : bond 0.03999 ( 106) hydrogen bonds : angle 5.56692 ( 306) link_BETA1-4 : bond 0.00421 ( 2) link_BETA1-4 : angle 1.61448 ( 6) link_NAG-ASN : bond 0.00544 ( 2) link_NAG-ASN : angle 0.85055 ( 6) *********************** 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 114 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4111 (tt0) cc_final: 0.3741 (tt0) REVERT: B 127 GLN cc_start: 0.7876 (mt0) cc_final: 0.7560 (mt0) REVERT: B 172 MET cc_start: 0.8448 (tpt) cc_final: 0.8079 (tpt) REVERT: B 205 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: B 251 SER cc_start: 0.8801 (m) cc_final: 0.8452 (t) REVERT: B 289 SER cc_start: 0.9118 (t) cc_final: 0.8672 (p) REVERT: B 381 GLN cc_start: 0.8545 (tt0) cc_final: 0.8147 (pt0) REVERT: B 411 GLU cc_start: 0.8446 (tp30) cc_final: 0.8080 (tt0) REVERT: B 423 GLU cc_start: 0.7745 (pp20) cc_final: 0.6992 (tp30) REVERT: B 460 SER cc_start: 0.8458 (t) cc_final: 0.8177 (p) REVERT: B 488 SER cc_start: 0.8213 (t) cc_final: 0.7958 (p) outliers start: 15 outliers final: 7 residues processed: 106 average time/residue: 0.4009 time to fit residues: 44.7005 Evaluate side-chains 101 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 371 LEU 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 15 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.143491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107838 restraints weight = 5843.976| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.80 r_work: 0.3121 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4835 Z= 0.146 Angle : 0.606 9.254 6584 Z= 0.318 Chirality : 0.045 0.169 749 Planarity : 0.005 0.036 853 Dihedral : 6.010 55.720 727 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.28 % Allowed : 16.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.31), residues: 598 helix: -1.78 (0.43), residues: 124 sheet: -2.39 (0.40), residues: 126 loop : -1.93 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 54 TYR 0.012 0.001 TYR B 324 PHE 0.018 0.002 PHE B 497 TRP 0.007 0.001 TRP B 437 HIS 0.003 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4823) covalent geometry : angle 0.59384 ( 6556) SS BOND : bond 0.00503 ( 8) SS BOND : angle 2.19412 ( 16) hydrogen bonds : bond 0.03850 ( 106) hydrogen bonds : angle 5.48175 ( 306) link_BETA1-4 : bond 0.00381 ( 2) link_BETA1-4 : angle 1.74184 ( 6) link_NAG-ASN : bond 0.00780 ( 2) link_NAG-ASN : angle 1.19283 ( 6) *********************** 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 110 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ASN cc_start: 0.7677 (m-40) cc_final: 0.7375 (m110) REVERT: B 57 GLU cc_start: 0.4136 (tt0) cc_final: 0.3515 (tt0) REVERT: B 127 GLN cc_start: 0.7787 (mt0) cc_final: 0.7488 (mt0) REVERT: B 251 SER cc_start: 0.8792 (m) cc_final: 0.8590 (t) REVERT: B 289 SER cc_start: 0.9072 (t) cc_final: 0.8668 (m) REVERT: B 381 GLN cc_start: 0.8545 (tt0) cc_final: 0.8227 (pt0) REVERT: B 411 GLU cc_start: 0.8449 (tp30) cc_final: 0.8103 (tt0) REVERT: B 423 GLU cc_start: 0.7647 (pp20) cc_final: 0.6985 (tp30) REVERT: B 460 SER cc_start: 0.8364 (t) cc_final: 0.8065 (p) REVERT: B 464 MET cc_start: 0.8830 (mmm) cc_final: 0.8623 (mmp) REVERT: B 488 SER cc_start: 0.8165 (t) cc_final: 0.7892 (p) outliers start: 17 outliers final: 8 residues processed: 103 average time/residue: 0.3877 time to fit residues: 42.0843 Evaluate side-chains 98 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 326 THR 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 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.144407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108636 restraints weight = 5861.963| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.78 r_work: 0.3122 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4835 Z= 0.140 Angle : 0.591 7.868 6584 Z= 0.309 Chirality : 0.045 0.155 749 Planarity : 0.004 0.031 853 Dihedral : 5.898 54.256 727 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.51 % Allowed : 16.99 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.31), residues: 598 helix: -1.38 (0.45), residues: 124 sheet: -2.34 (0.38), residues: 135 loop : -1.86 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 205 TYR 0.013 0.001 TYR B 50 PHE 0.013 0.002 PHE B 68 TRP 0.006 0.001 TRP B 87 HIS 0.002 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4823) covalent geometry : angle 0.57941 ( 6556) SS BOND : bond 0.00484 ( 8) SS BOND : angle 2.23089 ( 16) hydrogen bonds : bond 0.03584 ( 106) hydrogen bonds : angle 5.36207 ( 306) link_BETA1-4 : bond 0.00402 ( 2) link_BETA1-4 : angle 1.46182 ( 6) link_NAG-ASN : bond 0.00576 ( 2) link_NAG-ASN : angle 0.83186 ( 6) *********************** 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 107 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4188 (tt0) cc_final: 0.3492 (tt0) REVERT: B 127 GLN cc_start: 0.7732 (mt0) cc_final: 0.7468 (mt0) REVERT: B 156 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7700 (tmtt) REVERT: B 172 MET cc_start: 0.8322 (tpt) cc_final: 0.7977 (ttt) REVERT: B 251 SER cc_start: 0.8737 (m) cc_final: 0.8483 (t) REVERT: B 289 SER cc_start: 0.9004 (t) cc_final: 0.8598 (m) REVERT: B 381 GLN cc_start: 0.8556 (tt0) cc_final: 0.8211 (pt0) REVERT: B 411 GLU cc_start: 0.8480 (tp30) cc_final: 0.8149 (tt0) REVERT: B 423 GLU cc_start: 0.7629 (pp20) cc_final: 0.6975 (tp30) REVERT: B 460 SER cc_start: 0.8377 (t) cc_final: 0.8076 (p) REVERT: B 488 SER cc_start: 0.8125 (t) cc_final: 0.7865 (p) outliers start: 13 outliers final: 9 residues processed: 99 average time/residue: 0.3942 time to fit residues: 41.1675 Evaluate side-chains 98 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 246 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109163 restraints weight = 5919.823| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.80 r_work: 0.3132 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4835 Z= 0.129 Angle : 0.576 8.419 6584 Z= 0.302 Chirality : 0.044 0.148 749 Planarity : 0.004 0.033 853 Dihedral : 5.798 54.454 727 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.28 % Allowed : 16.80 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.32), residues: 598 helix: -1.10 (0.45), residues: 130 sheet: -2.05 (0.39), residues: 129 loop : -1.74 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.012 0.001 TYR B 324 PHE 0.012 0.001 PHE B 68 TRP 0.008 0.001 TRP B 87 HIS 0.002 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4823) covalent geometry : angle 0.56807 ( 6556) SS BOND : bond 0.00341 ( 8) SS BOND : angle 1.89133 ( 16) hydrogen bonds : bond 0.03490 ( 106) hydrogen bonds : angle 5.09933 ( 306) link_BETA1-4 : bond 0.00328 ( 2) link_BETA1-4 : angle 1.34019 ( 6) link_NAG-ASN : bond 0.00502 ( 2) link_NAG-ASN : angle 0.83216 ( 6) *********************** 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 115 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4407 (tt0) cc_final: 0.3701 (tt0) REVERT: B 127 GLN cc_start: 0.7559 (mt0) cc_final: 0.7269 (mt0) REVERT: B 156 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7646 (tmtt) REVERT: B 251 SER cc_start: 0.8745 (m) cc_final: 0.8496 (t) REVERT: B 289 SER cc_start: 0.8864 (t) cc_final: 0.8449 (m) REVERT: B 381 GLN cc_start: 0.8477 (tt0) cc_final: 0.8192 (pt0) REVERT: B 411 GLU cc_start: 0.8270 (tp30) cc_final: 0.7913 (tt0) REVERT: B 460 SER cc_start: 0.8273 (t) cc_final: 0.7830 (p) REVERT: B 464 MET cc_start: 0.8750 (mmm) cc_final: 0.8451 (mmp) REVERT: B 488 SER cc_start: 0.7993 (t) cc_final: 0.7772 (p) outliers start: 17 outliers final: 9 residues processed: 102 average time/residue: 0.3754 time to fit residues: 40.4136 Evaluate side-chains 94 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.143393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107299 restraints weight = 5852.796| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.80 r_work: 0.3113 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4835 Z= 0.182 Angle : 0.619 8.607 6584 Z= 0.319 Chirality : 0.046 0.151 749 Planarity : 0.004 0.032 853 Dihedral : 5.907 54.910 727 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.67 % Allowed : 16.99 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.32), residues: 598 helix: -1.00 (0.45), residues: 130 sheet: -2.16 (0.38), residues: 135 loop : -1.59 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 132 TYR 0.015 0.002 TYR B 324 PHE 0.013 0.002 PHE B 68 TRP 0.011 0.001 TRP B 87 HIS 0.003 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 4823) covalent geometry : angle 0.60953 ( 6556) SS BOND : bond 0.00369 ( 8) SS BOND : angle 2.15548 ( 16) hydrogen bonds : bond 0.03786 ( 106) hydrogen bonds : angle 5.01829 ( 306) link_BETA1-4 : bond 0.00362 ( 2) link_BETA1-4 : angle 1.38202 ( 6) link_NAG-ASN : bond 0.00449 ( 2) link_NAG-ASN : angle 0.76778 ( 6) *********************** 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: 19 poor density : 89 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4324 (tt0) cc_final: 0.3254 (tt0) REVERT: B 126 ASP cc_start: 0.8707 (m-30) cc_final: 0.8426 (m-30) REVERT: B 127 GLN cc_start: 0.7561 (mt0) cc_final: 0.7282 (mt0) REVERT: B 156 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7684 (tmtt) REVERT: B 251 SER cc_start: 0.8766 (m) cc_final: 0.8477 (t) REVERT: B 289 SER cc_start: 0.8947 (t) cc_final: 0.8554 (m) REVERT: B 381 GLN cc_start: 0.8543 (tt0) cc_final: 0.8240 (pt0) REVERT: B 411 GLU cc_start: 0.8444 (tp30) cc_final: 0.8086 (tt0) REVERT: B 460 SER cc_start: 0.8355 (t) cc_final: 0.7942 (p) REVERT: B 464 MET cc_start: 0.8826 (mmm) cc_final: 0.8537 (mmp) REVERT: B 488 SER cc_start: 0.8177 (t) cc_final: 0.7890 (p) outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 0.3791 time to fit residues: 38.4017 Evaluate side-chains 96 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 246 THR 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 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 ASN ** 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 = 0.3713 r_free = 0.3713 target = 0.145193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108954 restraints weight = 5916.024| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.82 r_work: 0.3137 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4835 Z= 0.139 Angle : 0.618 9.300 6584 Z= 0.318 Chirality : 0.045 0.146 749 Planarity : 0.004 0.033 853 Dihedral : 5.874 54.584 727 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.32), residues: 598 helix: -0.83 (0.45), residues: 130 sheet: -2.19 (0.38), residues: 122 loop : -1.64 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.012 0.001 TYR B 50 PHE 0.012 0.001 PHE B 68 TRP 0.013 0.001 TRP B 87 HIS 0.005 0.001 HIS B 419 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4823) covalent geometry : angle 0.59991 ( 6556) SS BOND : bond 0.01106 ( 8) SS BOND : angle 2.98294 ( 16) hydrogen bonds : bond 0.03489 ( 106) hydrogen bonds : angle 4.92876 ( 306) link_BETA1-4 : bond 0.00377 ( 2) link_BETA1-4 : angle 1.38148 ( 6) link_NAG-ASN : bond 0.00483 ( 2) link_NAG-ASN : angle 0.71860 ( 6) *********************** 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 103 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4384 (tt0) cc_final: 0.3304 (tt0) REVERT: B 126 ASP cc_start: 0.8548 (m-30) cc_final: 0.8262 (m-30) REVERT: B 127 GLN cc_start: 0.7568 (mt0) cc_final: 0.7278 (mt0) REVERT: B 251 SER cc_start: 0.8776 (m) cc_final: 0.8462 (t) REVERT: B 289 SER cc_start: 0.8825 (t) cc_final: 0.8420 (m) REVERT: B 381 GLN cc_start: 0.8341 (tt0) cc_final: 0.8059 (pt0) REVERT: B 411 GLU cc_start: 0.8225 (tp30) cc_final: 0.7904 (tt0) REVERT: B 460 SER cc_start: 0.8259 (t) cc_final: 0.7833 (p) REVERT: B 464 MET cc_start: 0.8753 (mmm) cc_final: 0.8453 (mmp) REVERT: B 488 SER cc_start: 0.8063 (t) cc_final: 0.7821 (p) outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 0.4134 time to fit residues: 40.4622 Evaluate side-chains 95 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 326 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111117 restraints weight = 5842.262| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.79 r_work: 0.3161 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4835 Z= 0.118 Angle : 0.589 7.499 6584 Z= 0.300 Chirality : 0.044 0.155 749 Planarity : 0.004 0.032 853 Dihedral : 5.702 54.006 727 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.70 % Allowed : 18.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.33), residues: 598 helix: -0.37 (0.48), residues: 124 sheet: -2.18 (0.38), residues: 127 loop : -1.50 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.011 0.001 TYR B 50 PHE 0.011 0.001 PHE B 68 TRP 0.017 0.001 TRP B 87 HIS 0.002 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4823) covalent geometry : angle 0.57894 ( 6556) SS BOND : bond 0.00635 ( 8) SS BOND : angle 2.17490 ( 16) hydrogen bonds : bond 0.03330 ( 106) hydrogen bonds : angle 4.84963 ( 306) link_BETA1-4 : bond 0.00373 ( 2) link_BETA1-4 : angle 1.29769 ( 6) link_NAG-ASN : bond 0.00483 ( 2) link_NAG-ASN : angle 0.75491 ( 6) *********************** 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 104 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4435 (tt0) cc_final: 0.3155 (tt0) REVERT: B 126 ASP cc_start: 0.8539 (m-30) cc_final: 0.8251 (m-30) REVERT: B 127 GLN cc_start: 0.7553 (mt0) cc_final: 0.7274 (mt0) REVERT: B 129 ILE cc_start: 0.7945 (pt) cc_final: 0.7662 (pp) REVERT: B 156 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7674 (tmtt) REVERT: B 251 SER cc_start: 0.8729 (m) cc_final: 0.8421 (t) REVERT: B 289 SER cc_start: 0.8859 (t) cc_final: 0.8436 (m) REVERT: B 381 GLN cc_start: 0.8064 (tt0) cc_final: 0.7770 (pt0) REVERT: B 411 GLU cc_start: 0.8220 (tp30) cc_final: 0.7898 (tt0) REVERT: B 417 GLU cc_start: 0.7294 (tt0) cc_final: 0.6843 (tp30) REVERT: B 464 MET cc_start: 0.8736 (mmm) cc_final: 0.8472 (mmp) REVERT: B 488 SER cc_start: 0.8026 (t) cc_final: 0.7806 (p) REVERT: B 587 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6533 (mtm180) outliers start: 14 outliers final: 10 residues processed: 94 average time/residue: 0.4011 time to fit residues: 39.7774 Evaluate side-chains 95 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 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 42 optimal weight: 4.9990 chunk 11 optimal weight: 0.0070 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.145988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109983 restraints weight = 5837.668| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.78 r_work: 0.3152 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4835 Z= 0.133 Angle : 0.599 8.701 6584 Z= 0.305 Chirality : 0.044 0.147 749 Planarity : 0.004 0.032 853 Dihedral : 5.723 54.404 727 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.51 % Allowed : 19.69 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.33), residues: 598 helix: -0.22 (0.49), residues: 124 sheet: -2.09 (0.38), residues: 127 loop : -1.48 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 132 TYR 0.012 0.001 TYR B 50 PHE 0.012 0.001 PHE B 68 TRP 0.023 0.001 TRP B 87 HIS 0.002 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4823) covalent geometry : angle 0.58772 ( 6556) SS BOND : bond 0.00621 ( 8) SS BOND : angle 2.32556 ( 16) hydrogen bonds : bond 0.03403 ( 106) hydrogen bonds : angle 4.76694 ( 306) link_BETA1-4 : bond 0.00366 ( 2) link_BETA1-4 : angle 1.31351 ( 6) link_NAG-ASN : bond 0.00466 ( 2) link_NAG-ASN : angle 0.69523 ( 6) ********************** 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 100 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: B 35 ASP cc_start: 0.8752 (t0) cc_final: 0.7971 (t0) REVERT: B 57 GLU cc_start: 0.4512 (tt0) cc_final: 0.3292 (tt0) REVERT: B 126 ASP cc_start: 0.8606 (m-30) cc_final: 0.8319 (m-30) REVERT: B 127 GLN cc_start: 0.7530 (mt0) cc_final: 0.7262 (mt0) REVERT: B 129 ILE cc_start: 0.8021 (pt) cc_final: 0.7726 (pp) REVERT: B 251 SER cc_start: 0.8701 (m) cc_final: 0.8390 (t) REVERT: B 289 SER cc_start: 0.8983 (t) cc_final: 0.8511 (p) REVERT: B 381 GLN cc_start: 0.8077 (tt0) cc_final: 0.7818 (pt0) REVERT: B 411 GLU cc_start: 0.8373 (tp30) cc_final: 0.8049 (tt0) REVERT: B 417 GLU cc_start: 0.7309 (tt0) cc_final: 0.6870 (tp30) REVERT: B 488 SER cc_start: 0.8122 (t) cc_final: 0.7866 (p) outliers start: 13 outliers final: 11 residues processed: 89 average time/residue: 0.4039 time to fit residues: 37.8883 Evaluate side-chains 96 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 455 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 570 MET 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 4 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.146836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110646 restraints weight = 5896.742| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.82 r_work: 0.3158 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4835 Z= 0.123 Angle : 0.596 8.108 6584 Z= 0.301 Chirality : 0.044 0.151 749 Planarity : 0.004 0.032 853 Dihedral : 5.655 54.169 727 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.70 % Allowed : 19.88 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.33), residues: 598 helix: -0.14 (0.49), residues: 124 sheet: -2.08 (0.38), residues: 127 loop : -1.48 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 205 TYR 0.012 0.001 TYR B 50 PHE 0.011 0.001 PHE B 68 TRP 0.023 0.001 TRP B 87 HIS 0.002 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4823) covalent geometry : angle 0.58600 ( 6556) SS BOND : bond 0.00568 ( 8) SS BOND : angle 2.14443 ( 16) hydrogen bonds : bond 0.03298 ( 106) hydrogen bonds : angle 4.72541 ( 306) link_BETA1-4 : bond 0.00369 ( 2) link_BETA1-4 : angle 1.29989 ( 6) link_NAG-ASN : bond 0.00437 ( 2) link_NAG-ASN : angle 0.70339 ( 6) =============================================================================== Job complete usr+sys time: 1863.32 seconds wall clock time: 32 minutes 28.19 seconds (1948.19 seconds total)