Starting phenix.real_space_refine on Thu Jul 24 00:57:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u2k_20621/07_2025/6u2k_20621_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u2k_20621/07_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_20621/07_2025/6u2k_20621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u2k_20621/07_2025/6u2k_20621.map" model { file = "/net/cci-nas-00/data/ceres_data/6u2k_20621/07_2025/6u2k_20621_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u2k_20621/07_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-5711/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: 3.29, per 1000 atoms: 0.70 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: 1.18 Conformation dependent library (CDL) restraints added in 581.5 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: 0.57 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: 1.41 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: 0.310 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.330 Find NCS groups from input model: 0.050 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:16.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.460 ------------------------------------------------------------------------------- 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 : 3.34 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00926 ( 2) link_NAG-ASN : angle 1.73996 ( 6) link_BETA1-4 : bond 0.00592 ( 2) link_BETA1-4 : angle 3.11337 ( 6) hydrogen bonds : bond 0.31965 ( 106) hydrogen bonds : angle 10.46826 ( 306) SS BOND : bond 0.00426 ( 8) SS BOND : angle 1.33140 ( 16) covalent geometry : bond 0.01007 ( 4823) covalent geometry : angle 0.98937 ( 6556) *********************** 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 : 0.504 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: 0.9250 time to fit residues: 135.6899 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 : 0.576 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.0270 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.141653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105797 restraints weight = 5701.367| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.77 r_work: 0.3129 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4835 Z= 0.140 Angle : 0.633 6.660 6584 Z= 0.338 Chirality : 0.046 0.221 749 Planarity : 0.006 0.042 853 Dihedral : 7.297 56.071 727 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.28 % Allowed : 11.39 % 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: -3.81 (0.29), residues: 598 helix: -3.22 (0.34), residues: 119 sheet: -2.80 (0.39), residues: 117 loop : -2.22 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 275 HIS 0.003 0.001 HIS B 282 PHE 0.016 0.002 PHE B 68 TYR 0.015 0.002 TYR B 50 ARG 0.003 0.000 ARG B 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00776 ( 2) link_NAG-ASN : angle 1.41949 ( 6) link_BETA1-4 : bond 0.00443 ( 2) link_BETA1-4 : angle 2.28873 ( 6) hydrogen bonds : bond 0.04429 ( 106) hydrogen bonds : angle 6.02338 ( 306) SS BOND : bond 0.00325 ( 8) SS BOND : angle 1.41174 ( 16) covalent geometry : bond 0.00319 ( 4823) covalent geometry : angle 0.62548 ( 6556) *********************** 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: 17 poor density : 102 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 14 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7673 (p) REVERT: B 79 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8481 (mmm) REVERT: B 127 GLN cc_start: 0.7812 (mt0) cc_final: 0.7301 (mt0) REVERT: B 289 SER cc_start: 0.9122 (t) cc_final: 0.8686 (p) REVERT: B 333 CYS cc_start: 0.7922 (t) cc_final: 0.7713 (t) REVERT: B 381 GLN cc_start: 0.8607 (tt0) cc_final: 0.8185 (pt0) REVERT: B 411 GLU cc_start: 0.8382 (tp30) cc_final: 0.8033 (tt0) REVERT: B 423 GLU cc_start: 0.7835 (pp20) cc_final: 0.6914 (tp30) REVERT: B 460 SER cc_start: 0.8537 (t) cc_final: 0.8203 (p) REVERT: B 481 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: B 482 ASN cc_start: 0.8310 (m110) cc_final: 0.7920 (m-40) REVERT: B 488 SER cc_start: 0.8228 (t) cc_final: 0.7949 (p) outliers start: 17 outliers final: 8 residues processed: 112 average time/residue: 1.0825 time to fit residues: 127.3923 Evaluate side-chains 105 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.143494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.107752 restraints weight = 5773.339| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.79 r_work: 0.3091 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4835 Z= 0.127 Angle : 0.578 7.273 6584 Z= 0.307 Chirality : 0.044 0.159 749 Planarity : 0.005 0.034 853 Dihedral : 6.400 55.354 727 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.90 % Allowed : 14.86 % Favored : 82.24 % 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: -3.29 (0.30), residues: 598 helix: -2.23 (0.41), residues: 124 sheet: -2.56 (0.39), residues: 126 loop : -2.02 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 437 HIS 0.002 0.001 HIS B 203 PHE 0.014 0.001 PHE B 480 TYR 0.011 0.001 TYR B 324 ARG 0.003 0.000 ARG B 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 2) link_NAG-ASN : angle 0.83841 ( 6) link_BETA1-4 : bond 0.00266 ( 2) link_BETA1-4 : angle 1.60180 ( 6) hydrogen bonds : bond 0.03908 ( 106) hydrogen bonds : angle 5.54508 ( 306) SS BOND : bond 0.00340 ( 8) SS BOND : angle 1.67100 ( 16) covalent geometry : bond 0.00297 ( 4823) covalent geometry : angle 0.57044 ( 6556) *********************** 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 118 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4103 (tt0) cc_final: 0.3785 (tt0) REVERT: B 127 GLN cc_start: 0.7869 (mt0) cc_final: 0.7555 (mt0) REVERT: B 172 MET cc_start: 0.8396 (tpt) cc_final: 0.8021 (tpt) REVERT: B 205 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7748 (ttm-80) REVERT: B 251 SER cc_start: 0.8787 (m) cc_final: 0.8434 (t) REVERT: B 289 SER cc_start: 0.9112 (t) cc_final: 0.8661 (p) REVERT: B 381 GLN cc_start: 0.8554 (tt0) cc_final: 0.8147 (pt0) REVERT: B 411 GLU cc_start: 0.8437 (tp30) cc_final: 0.8072 (tt0) REVERT: B 423 GLU cc_start: 0.7693 (pp20) cc_final: 0.6976 (tp30) REVERT: B 460 SER cc_start: 0.8425 (t) cc_final: 0.8145 (p) REVERT: B 488 SER cc_start: 0.8200 (t) cc_final: 0.7948 (p) outliers start: 15 outliers final: 8 residues processed: 109 average time/residue: 0.8166 time to fit residues: 93.9718 Evaluate side-chains 103 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 386 LYS 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: 3.9990 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.143579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107858 restraints weight = 5836.662| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.80 r_work: 0.3119 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 4835 Z= 0.151 Angle : 0.610 9.631 6584 Z= 0.319 Chirality : 0.045 0.188 749 Planarity : 0.004 0.035 853 Dihedral : 6.017 55.671 727 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.28 % Allowed : 15.83 % Favored : 80.89 % 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: -3.00 (0.31), residues: 598 helix: -1.77 (0.44), residues: 124 sheet: -2.40 (0.40), residues: 126 loop : -1.92 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 437 HIS 0.003 0.001 HIS B 282 PHE 0.018 0.002 PHE B 497 TYR 0.013 0.001 TYR B 324 ARG 0.005 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00863 ( 2) link_NAG-ASN : angle 1.33981 ( 6) link_BETA1-4 : bond 0.00358 ( 2) link_BETA1-4 : angle 1.78403 ( 6) hydrogen bonds : bond 0.03868 ( 106) hydrogen bonds : angle 5.48227 ( 306) SS BOND : bond 0.00438 ( 8) SS BOND : angle 2.30714 ( 16) covalent geometry : bond 0.00362 ( 4823) covalent geometry : angle 0.59686 ( 6556) *********************** 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 111 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ASN cc_start: 0.7711 (m-40) cc_final: 0.7407 (m110) REVERT: B 57 GLU cc_start: 0.4443 (tt0) cc_final: 0.3856 (tt0) REVERT: B 127 GLN cc_start: 0.7825 (mt0) cc_final: 0.7530 (mt0) REVERT: B 156 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7750 (tmtt) REVERT: B 251 SER cc_start: 0.8806 (m) cc_final: 0.8598 (t) REVERT: B 289 SER cc_start: 0.9106 (t) cc_final: 0.8711 (m) REVERT: B 381 GLN cc_start: 0.8564 (tt0) cc_final: 0.8229 (pt0) REVERT: B 411 GLU cc_start: 0.8482 (tp30) cc_final: 0.8074 (tt0) REVERT: B 423 GLU cc_start: 0.7717 (pp20) cc_final: 0.7019 (tp30) REVERT: B 460 SER cc_start: 0.8422 (t) cc_final: 0.8127 (p) REVERT: B 488 SER cc_start: 0.8185 (t) cc_final: 0.7910 (p) outliers start: 17 outliers final: 7 residues processed: 102 average time/residue: 1.0280 time to fit residues: 111.6759 Evaluate side-chains 93 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 43 optimal weight: 0.0980 chunk 14 optimal weight: 0.0570 chunk 23 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.146689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111012 restraints weight = 5904.245| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.80 r_work: 0.3163 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4835 Z= 0.109 Angle : 0.568 8.011 6584 Z= 0.298 Chirality : 0.043 0.158 749 Planarity : 0.004 0.032 853 Dihedral : 5.779 53.967 727 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.70 % Allowed : 16.99 % Favored : 80.31 % 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: -2.68 (0.32), residues: 598 helix: -1.38 (0.44), residues: 130 sheet: -2.29 (0.40), residues: 125 loop : -1.72 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 275 HIS 0.002 0.000 HIS B 203 PHE 0.012 0.001 PHE B 68 TYR 0.013 0.001 TYR B 50 ARG 0.004 0.000 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 2) link_NAG-ASN : angle 0.91337 ( 6) link_BETA1-4 : bond 0.00305 ( 2) link_BETA1-4 : angle 1.40411 ( 6) hydrogen bonds : bond 0.03291 ( 106) hydrogen bonds : angle 5.29498 ( 306) SS BOND : bond 0.00521 ( 8) SS BOND : angle 2.37587 ( 16) covalent geometry : bond 0.00259 ( 4823) covalent geometry : angle 0.55464 ( 6556) *********************** 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 112 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.4393 (tt0) cc_final: 0.3897 (tt0) REVERT: B 101 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 127 GLN cc_start: 0.7746 (mt0) cc_final: 0.7451 (mt0) REVERT: B 156 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7651 (tmtt) REVERT: B 172 MET cc_start: 0.8031 (tpt) cc_final: 0.7586 (ttt) REVERT: B 251 SER cc_start: 0.8737 (m) cc_final: 0.8500 (t) REVERT: B 289 SER cc_start: 0.8881 (t) cc_final: 0.8472 (m) REVERT: B 333 CYS cc_start: 0.7649 (t) cc_final: 0.7030 (t) REVERT: B 381 GLN cc_start: 0.8478 (tt0) cc_final: 0.8176 (pt0) REVERT: B 411 GLU cc_start: 0.8246 (tp30) cc_final: 0.7845 (tt0) REVERT: B 460 SER cc_start: 0.8269 (t) cc_final: 0.7840 (p) REVERT: B 488 SER cc_start: 0.8005 (t) cc_final: 0.7790 (p) outliers start: 14 outliers final: 8 residues processed: 102 average time/residue: 1.3602 time to fit residues: 145.7182 Evaluate side-chains 96 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 149 GLU 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 54 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.145054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109318 restraints weight = 5850.957| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.79 r_work: 0.3132 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4835 Z= 0.139 Angle : 0.591 8.477 6584 Z= 0.306 Chirality : 0.045 0.148 749 Planarity : 0.004 0.033 853 Dihedral : 5.777 54.457 727 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.51 % Allowed : 18.34 % Favored : 79.15 % 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: -2.50 (0.33), residues: 598 helix: -1.05 (0.45), residues: 130 sheet: -2.17 (0.38), residues: 134 loop : -1.65 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.002 0.001 HIS B 282 PHE 0.013 0.001 PHE B 68 TYR 0.013 0.001 TYR B 324 ARG 0.004 0.000 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 2) link_NAG-ASN : angle 0.84682 ( 6) link_BETA1-4 : bond 0.00431 ( 2) link_BETA1-4 : angle 1.34148 ( 6) hydrogen bonds : bond 0.03499 ( 106) hydrogen bonds : angle 5.10461 ( 306) SS BOND : bond 0.00360 ( 8) SS BOND : angle 2.05921 ( 16) covalent geometry : bond 0.00333 ( 4823) covalent geometry : angle 0.58181 ( 6556) *********************** 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 106 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.642 Fit side-chains REVERT: B 57 GLU cc_start: 0.4249 (tt0) cc_final: 0.3652 (tt0) REVERT: B 79 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8499 (mmm) REVERT: B 127 GLN cc_start: 0.7611 (mt0) cc_final: 0.7340 (mt0) REVERT: B 156 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7698 (tmtt) REVERT: B 172 MET cc_start: 0.8412 (tpt) cc_final: 0.7901 (ttt) REVERT: B 251 SER cc_start: 0.8723 (m) cc_final: 0.8481 (t) REVERT: B 289 SER cc_start: 0.8997 (t) cc_final: 0.8603 (m) REVERT: B 381 GLN cc_start: 0.8563 (tt0) cc_final: 0.8266 (pt0) REVERT: B 411 GLU cc_start: 0.8476 (tp30) cc_final: 0.8103 (tt0) REVERT: B 460 SER cc_start: 0.8340 (t) cc_final: 0.7940 (p) REVERT: B 488 SER cc_start: 0.8082 (t) cc_final: 0.7849 (p) outliers start: 13 outliers final: 9 residues processed: 95 average time/residue: 0.8947 time to fit residues: 89.9949 Evaluate side-chains 96 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 79 MET 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 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.144439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108400 restraints weight = 5863.727| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.81 r_work: 0.3122 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4835 Z= 0.158 Angle : 0.631 9.301 6584 Z= 0.324 Chirality : 0.046 0.148 749 Planarity : 0.004 0.032 853 Dihedral : 5.858 54.599 727 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % 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: -2.41 (0.33), residues: 598 helix: -0.78 (0.47), residues: 124 sheet: -2.30 (0.37), residues: 127 loop : -1.62 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 87 HIS 0.004 0.001 HIS B 419 PHE 0.012 0.002 PHE B 68 TYR 0.013 0.001 TYR B 324 ARG 0.003 0.000 ARG B 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 2) link_NAG-ASN : angle 0.81217 ( 6) link_BETA1-4 : bond 0.00338 ( 2) link_BETA1-4 : angle 1.33842 ( 6) hydrogen bonds : bond 0.03609 ( 106) hydrogen bonds : angle 5.00338 ( 306) SS BOND : bond 0.00779 ( 8) SS BOND : angle 3.07301 ( 16) covalent geometry : bond 0.00380 ( 4823) covalent geometry : angle 0.61190 ( 6556) *********************** 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 102 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.564 Fit side-chains REVERT: B 57 GLU cc_start: 0.4234 (tt0) cc_final: 0.3283 (tt0) REVERT: B 126 ASP cc_start: 0.8598 (m-30) cc_final: 0.8314 (m-30) REVERT: B 127 GLN cc_start: 0.7574 (mt0) cc_final: 0.7286 (mt0) REVERT: B 156 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7590 (tmtt) REVERT: B 251 SER cc_start: 0.8711 (m) cc_final: 0.8438 (t) REVERT: B 289 SER cc_start: 0.8836 (t) cc_final: 0.8408 (m) REVERT: B 381 GLN cc_start: 0.8452 (tt0) cc_final: 0.8145 (pt0) REVERT: B 411 GLU cc_start: 0.8263 (tp30) cc_final: 0.7895 (tt0) REVERT: B 460 SER cc_start: 0.8231 (t) cc_final: 0.7808 (p) REVERT: B 488 SER cc_start: 0.8042 (t) cc_final: 0.7792 (p) outliers start: 18 outliers final: 11 residues processed: 90 average time/residue: 0.8685 time to fit residues: 82.5204 Evaluate side-chains 93 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 555 SER 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: 1.9990 chunk 1 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.146944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111257 restraints weight = 5849.661| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.79 r_work: 0.3167 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4835 Z= 0.112 Angle : 0.567 7.927 6584 Z= 0.294 Chirality : 0.043 0.153 749 Planarity : 0.004 0.032 853 Dihedral : 5.668 53.843 727 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.51 % Allowed : 19.31 % Favored : 78.19 % 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: -2.25 (0.33), residues: 598 helix: -0.59 (0.47), residues: 130 sheet: -2.14 (0.38), residues: 127 loop : -1.58 (0.34), 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 203 PHE 0.011 0.001 PHE B 497 TYR 0.010 0.001 TYR B 50 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 2) link_NAG-ASN : angle 0.84178 ( 6) link_BETA1-4 : bond 0.00405 ( 2) link_BETA1-4 : angle 1.29769 ( 6) hydrogen bonds : bond 0.03236 ( 106) hydrogen bonds : angle 4.86704 ( 306) SS BOND : bond 0.00683 ( 8) SS BOND : angle 2.22116 ( 16) covalent geometry : bond 0.00262 ( 4823) covalent geometry : angle 0.55550 ( 6556) *********************** 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: 13 poor density : 92 time to evaluate : 0.488 Fit side-chains REVERT: B 57 GLU cc_start: 0.4266 (tt0) cc_final: 0.3257 (tt0) REVERT: B 126 ASP cc_start: 0.8533 (m-30) cc_final: 0.8139 (m-30) REVERT: B 127 GLN cc_start: 0.7540 (mt0) cc_final: 0.7259 (mt0) REVERT: B 129 ILE cc_start: 0.7923 (pt) cc_final: 0.7621 (pp) REVERT: B 251 SER cc_start: 0.8710 (m) cc_final: 0.8434 (t) REVERT: B 289 SER cc_start: 0.8813 (t) cc_final: 0.8389 (m) REVERT: B 381 GLN cc_start: 0.8380 (tt0) cc_final: 0.8101 (pt0) REVERT: B 411 GLU cc_start: 0.8212 (tp30) cc_final: 0.7903 (tt0) REVERT: B 417 GLU cc_start: 0.7318 (tt0) cc_final: 0.6876 (tp30) REVERT: B 464 MET cc_start: 0.8718 (mmm) cc_final: 0.8415 (mmp) REVERT: B 488 SER cc_start: 0.7989 (t) cc_final: 0.7775 (p) REVERT: B 536 ILE cc_start: 0.8362 (mp) cc_final: 0.8141 (mp) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.8558 time to fit residues: 87.9844 Evaluate side-chains 94 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 336 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 579 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.146697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111173 restraints weight = 5860.536| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.77 r_work: 0.3166 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4835 Z= 0.118 Angle : 0.588 9.397 6584 Z= 0.301 Chirality : 0.044 0.152 749 Planarity : 0.004 0.032 853 Dihedral : 5.629 54.162 727 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.90 % Allowed : 20.46 % Favored : 76.64 % 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: -2.08 (0.33), residues: 598 helix: -0.28 (0.49), residues: 124 sheet: -2.04 (0.38), residues: 127 loop : -1.53 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 87 HIS 0.002 0.001 HIS B 282 PHE 0.012 0.001 PHE B 68 TYR 0.011 0.001 TYR B 50 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 2) link_NAG-ASN : angle 0.83537 ( 6) link_BETA1-4 : bond 0.00382 ( 2) link_BETA1-4 : angle 1.26831 ( 6) hydrogen bonds : bond 0.03293 ( 106) hydrogen bonds : angle 4.81915 ( 306) SS BOND : bond 0.00612 ( 8) SS BOND : angle 2.29545 ( 16) covalent geometry : bond 0.00278 ( 4823) covalent geometry : angle 0.57633 ( 6556) *********************** 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: 15 poor density : 89 time to evaluate : 0.503 Fit side-chains REVERT: B 57 GLU cc_start: 0.4443 (tt0) cc_final: 0.3415 (tt0) REVERT: B 126 ASP cc_start: 0.8611 (m-30) cc_final: 0.8324 (m-30) REVERT: B 127 GLN cc_start: 0.7537 (mt0) cc_final: 0.7269 (mt0) REVERT: B 129 ILE cc_start: 0.7976 (pt) cc_final: 0.7649 (pp) REVERT: B 156 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7690 (tmtt) REVERT: B 251 SER cc_start: 0.8687 (m) cc_final: 0.8369 (t) REVERT: B 289 SER cc_start: 0.8940 (t) cc_final: 0.8459 (p) REVERT: B 381 GLN cc_start: 0.8353 (tt0) cc_final: 0.8049 (pt0) REVERT: B 411 GLU cc_start: 0.8405 (tp30) cc_final: 0.8108 (tt0) REVERT: B 417 GLU cc_start: 0.7298 (tt0) cc_final: 0.6874 (tp30) REVERT: B 424 ASP cc_start: 0.7928 (p0) cc_final: 0.7608 (p0) REVERT: B 464 MET cc_start: 0.8807 (mmm) cc_final: 0.8519 (mmp) REVERT: B 488 SER cc_start: 0.8057 (t) cc_final: 0.7830 (p) REVERT: B 536 ILE cc_start: 0.8493 (mp) cc_final: 0.8291 (mp) outliers start: 15 outliers final: 11 residues processed: 94 average time/residue: 0.8861 time to fit residues: 87.9265 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 : 0.550 ------------------------------------------------------------------------------- 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 555 SER 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: 2.9990 chunk 35 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.0170 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.147065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111134 restraints weight = 5886.013| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.79 r_work: 0.3168 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4835 Z= 0.117 Angle : 0.588 9.255 6584 Z= 0.300 Chirality : 0.044 0.150 749 Planarity : 0.004 0.032 853 Dihedral : 5.596 54.046 727 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.32 % Allowed : 21.62 % Favored : 76.06 % 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: -2.00 (0.33), residues: 598 helix: -0.12 (0.50), residues: 123 sheet: -1.98 (0.38), residues: 127 loop : -1.52 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 87 HIS 0.001 0.001 HIS B 282 PHE 0.012 0.001 PHE B 497 TYR 0.011 0.001 TYR B 50 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 2) link_NAG-ASN : angle 0.77766 ( 6) link_BETA1-4 : bond 0.00362 ( 2) link_BETA1-4 : angle 1.26875 ( 6) hydrogen bonds : bond 0.03232 ( 106) hydrogen bonds : angle 4.82020 ( 306) SS BOND : bond 0.00564 ( 8) SS BOND : angle 2.23074 ( 16) covalent geometry : bond 0.00276 ( 4823) covalent geometry : angle 0.57677 ( 6556) ********************** 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: 12 poor density : 88 time to evaluate : 0.547 Fit side-chains REVERT: B 57 GLU cc_start: 0.4531 (tt0) cc_final: 0.3545 (tt0) REVERT: B 126 ASP cc_start: 0.8583 (m-30) cc_final: 0.8195 (m-30) REVERT: B 127 GLN cc_start: 0.7522 (mt0) cc_final: 0.7244 (mt0) REVERT: B 129 ILE cc_start: 0.7970 (pt) cc_final: 0.7696 (pp) REVERT: B 251 SER cc_start: 0.8582 (m) cc_final: 0.8251 (t) REVERT: B 289 SER cc_start: 0.8940 (t) cc_final: 0.8464 (p) REVERT: B 381 GLN cc_start: 0.8310 (tt0) cc_final: 0.8064 (pt0) REVERT: B 411 GLU cc_start: 0.8389 (tp30) cc_final: 0.8075 (tt0) REVERT: B 417 GLU cc_start: 0.7295 (tt0) cc_final: 0.6867 (tp30) REVERT: B 464 MET cc_start: 0.8822 (mmm) cc_final: 0.8528 (mmp) REVERT: B 488 SER cc_start: 0.8059 (t) cc_final: 0.7821 (p) REVERT: B 536 ILE cc_start: 0.8477 (mp) cc_final: 0.8277 (mp) outliers start: 12 outliers final: 10 residues processed: 91 average time/residue: 0.8296 time to fit residues: 79.6739 Evaluate side-chains 96 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 555 SER 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 28 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN B 374 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 = 0.3731 r_free = 0.3731 target = 0.146227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110269 restraints weight = 5909.277| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.79 r_work: 0.3154 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4835 Z= 0.137 Angle : 0.608 9.140 6584 Z= 0.309 Chirality : 0.044 0.149 749 Planarity : 0.004 0.032 853 Dihedral : 5.649 54.339 727 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.70 % Allowed : 21.24 % Favored : 76.06 % 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: -2.00 (0.33), residues: 598 helix: -0.02 (0.50), residues: 121 sheet: -2.03 (0.38), residues: 127 loop : -1.54 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 87 HIS 0.002 0.001 HIS B 282 PHE 0.012 0.001 PHE B 68 TYR 0.011 0.001 TYR B 50 ARG 0.004 0.000 ARG B 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 2) link_NAG-ASN : angle 0.74128 ( 6) link_BETA1-4 : bond 0.00341 ( 2) link_BETA1-4 : angle 1.28039 ( 6) hydrogen bonds : bond 0.03401 ( 106) hydrogen bonds : angle 4.84065 ( 306) SS BOND : bond 0.00536 ( 8) SS BOND : angle 2.06368 ( 16) covalent geometry : bond 0.00327 ( 4823) covalent geometry : angle 0.59910 ( 6556) =============================================================================== Job complete usr+sys time: 4458.72 seconds wall clock time: 80 minutes 29.24 seconds (4829.24 seconds total)