Starting phenix.real_space_refine on Thu Jun 5 09:35:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ip7_60764/06_2025/9ip7_60764.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ip7_60764/06_2025/9ip7_60764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ip7_60764/06_2025/9ip7_60764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ip7_60764/06_2025/9ip7_60764.map" model { file = "/net/cci-nas-00/data/ceres_data/9ip7_60764/06_2025/9ip7_60764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ip7_60764/06_2025/9ip7_60764.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 55 5.16 5 C 3634 2.51 5 N 1002 2.21 5 O 1118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5809 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3938 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 23, 'TRANS': 484} Chain breaks: 7 Chain: "D" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 13, 'TRANS': 216} Chain breaks: 1 Chain: "B" 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 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 Time building chain proxies: 4.31, per 1000 atoms: 0.74 Number of scatterers: 5809 At special positions: 0 Unit cell: (67.768, 110.32, 123.716, 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 55 16.00 O 1118 8.00 N 1002 7.00 C 3634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 34 " distance=2.02 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 531 " distance=2.04 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 223 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 363 " distance=2.03 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 B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 701 " - " ASN A 337 " " NAG A 702 " - " ASN A 504 " " NAG B 1 " - " ASN A 328 " " NAG C 1 " - " ASN A 420 " Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 751.8 milliseconds 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 15 sheets defined 8.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 Processing helix chain 'A' and resid 318 through 322 removed outlier: 4.249A pdb=" N PHE A 321 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 removed outlier: 3.759A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.547A pdb=" N ASP A 369 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 407 through 410 Processing helix chain 'A' and resid 471 through 478 Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.755A pdb=" N TYR D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 354 through 358 removed outlier: 4.012A pdb=" N THR D 358 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 294 Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA7, first strand: chain 'A' and resid 346 through 347 removed outlier: 7.681A pdb=" N LEU A 381 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 524 through 526 Processing sheet with id=AA9, first strand: chain 'A' and resid 562 through 563 Processing sheet with id=AB1, first strand: chain 'D' and resid 134 through 136 Processing sheet with id=AB2, first strand: chain 'D' and resid 180 through 183 removed outlier: 6.524A pdb=" N TRP D 170 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 270 through 273 removed outlier: 3.505A pdb=" N SER D 292 " --> pdb=" O GLN D 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 277 through 279 removed outlier: 3.656A pdb=" N ALA D 359 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AB6, first strand: chain 'D' and resid 304 through 306 91 hydrogen bonds defined for protein. 189 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: 1.38 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 971 1.32 - 1.44: 1563 1.44 - 1.57: 3321 1.57 - 1.69: 0 1.69 - 1.82: 70 Bond restraints: 5925 Sorted by residual: bond pdb=" N GLY A 315 " pdb=" CA GLY A 315 " ideal model delta sigma weight residual 1.444 1.481 -0.037 9.60e-03 1.09e+04 1.45e+01 bond pdb=" N VAL A 284 " pdb=" CA VAL A 284 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.29e+01 bond pdb=" N ILE A 316 " pdb=" CA ILE A 316 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.10e-02 8.26e+03 1.24e+01 bond pdb=" N ILE A 401 " pdb=" CA ILE A 401 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.14e-02 7.69e+03 1.22e+01 bond pdb=" N VAL A 97 " pdb=" CA VAL A 97 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.23e-02 6.61e+03 1.16e+01 ... (remaining 5920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 7138 1.82 - 3.63: 762 3.63 - 5.45: 101 5.45 - 7.26: 7 7.26 - 9.08: 2 Bond angle restraints: 8010 Sorted by residual: angle pdb=" N GLY A 281 " pdb=" CA GLY A 281 " pdb=" C GLY A 281 " ideal model delta sigma weight residual 115.27 108.60 6.67 1.41e+00 5.03e-01 2.24e+01 angle pdb=" N HIS A 334 " pdb=" CA HIS A 334 " pdb=" C HIS A 334 " ideal model delta sigma weight residual 112.38 106.87 5.51 1.22e+00 6.72e-01 2.04e+01 angle pdb=" CA GLY A 520 " pdb=" C GLY A 520 " pdb=" O GLY A 520 " ideal model delta sigma weight residual 122.14 117.67 4.47 1.05e+00 9.07e-01 1.81e+01 angle pdb=" CA GLY A 490 " pdb=" C GLY A 490 " pdb=" O GLY A 490 " ideal model delta sigma weight residual 121.76 118.07 3.69 8.70e-01 1.32e+00 1.80e+01 angle pdb=" CA ILE A 451 " pdb=" C ILE A 451 " pdb=" O ILE A 451 " ideal model delta sigma weight residual 121.58 117.54 4.04 1.00e+00 1.00e+00 1.64e+01 ... (remaining 8005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3133 17.80 - 35.60: 403 35.60 - 53.40: 105 53.40 - 71.19: 39 71.19 - 88.99: 9 Dihedral angle restraints: 3689 sinusoidal: 1583 harmonic: 2106 Sorted by residual: dihedral pdb=" CB CYS A 271 " pdb=" SG CYS A 271 " pdb=" SG CYS A 283 " pdb=" CB CYS A 283 " ideal model delta sinusoidal sigma weight residual 93.00 -178.01 -88.99 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS A 7 " pdb=" SG CYS A 7 " pdb=" SG CYS A 34 " pdb=" CB CYS A 34 " ideal model delta sinusoidal sigma weight residual 93.00 161.99 -68.99 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS A 515 " pdb=" SG CYS A 515 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual -86.00 -146.53 60.53 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 3686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 731 0.093 - 0.186: 153 0.186 - 0.280: 11 0.280 - 0.373: 0 0.373 - 0.466: 1 Chirality restraints: 896 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.05e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA ILE A 119 " pdb=" N ILE A 119 " pdb=" C ILE A 119 " pdb=" CB ILE A 119 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 893 not shown) Planarity restraints: 1033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.274 2.00e-02 2.50e+03 2.30e-01 6.61e+02 pdb=" C7 NAG C 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.390 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.192 2.00e-02 2.50e+03 1.60e-01 3.21e+02 pdb=" C7 NAG C 1 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.138 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.264 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 315 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C MET D 315 " -0.046 2.00e-02 2.50e+03 pdb=" O MET D 315 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY D 316 " 0.016 2.00e-02 2.50e+03 ... (remaining 1030 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 809 2.76 - 3.29: 5899 3.29 - 3.83: 9957 3.83 - 4.36: 12373 4.36 - 4.90: 19970 Nonbonded interactions: 49008 Sorted by model distance: nonbonded pdb=" O CYS A 287 " pdb=" OG SER A 291 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP A 232 " pdb=" N GLU A 233 " model vdw 2.237 3.120 nonbonded pdb=" N ARG A 231 " pdb=" O ALA A 265 " model vdw 2.275 3.120 nonbonded pdb=" O SER A 529 " pdb=" OG SER A 529 " model vdw 2.304 3.040 nonbonded pdb=" O CYS A 313 " pdb=" N SER A 342 " model vdw 2.318 3.120 ... (remaining 49003 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 'B' 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.730 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 : 0.008 0.046 5949 Z= 0.611 Angle : 1.112 10.596 8064 Z= 0.761 Chirality : 0.070 0.466 896 Planarity : 0.011 0.230 1029 Dihedral : 17.204 87.035 2283 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 3.12 % Allowed : 31.67 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.31), residues: 718 helix: -1.05 (1.10), residues: 22 sheet: -2.72 (0.45), residues: 106 loop : -1.37 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 375 HIS 0.005 0.001 HIS A 359 PHE 0.018 0.002 PHE D 371 TYR 0.017 0.002 TYR D 184 ARG 0.006 0.001 ARG A 228 Details of bonding type rmsd link_NAG-ASN : bond 0.00844 ( 4) link_NAG-ASN : angle 3.85896 ( 12) link_BETA1-4 : bond 0.03266 ( 2) link_BETA1-4 : angle 4.59508 ( 6) hydrogen bonds : bond 0.24809 ( 91) hydrogen bonds : angle 11.76019 ( 189) SS BOND : bond 0.00396 ( 18) SS BOND : angle 0.98439 ( 36) covalent geometry : bond 0.00838 ( 5925) covalent geometry : angle 1.09654 ( 8010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.7976 (t80) cc_final: 0.7575 (t80) REVERT: A 152 MET cc_start: 0.7168 (pmm) cc_final: 0.6669 (pmm) REVERT: A 272 PRO cc_start: 0.7841 (OUTLIER) cc_final: 0.7631 (Cg_exo) REVERT: A 275 TYR cc_start: 0.4616 (m-10) cc_final: 0.4180 (m-10) REVERT: D 299 TYR cc_start: 0.7764 (m-80) cc_final: 0.7423 (m-80) outliers start: 20 outliers final: 6 residues processed: 114 average time/residue: 0.2469 time to fit residues: 35.0265 Evaluate side-chains 87 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 272 PRO Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 524 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.226580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.172211 restraints weight = 7466.006| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.77 r_work: 0.4112 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5949 Z= 0.138 Angle : 0.652 9.532 8064 Z= 0.317 Chirality : 0.049 0.427 896 Planarity : 0.004 0.042 1029 Dihedral : 6.440 44.136 929 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.99 % Allowed : 30.11 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.31), residues: 718 helix: 0.75 (1.25), residues: 16 sheet: -2.35 (0.44), residues: 120 loop : -1.19 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 140 HIS 0.007 0.001 HIS D 228 PHE 0.016 0.002 PHE D 371 TYR 0.020 0.002 TYR D 184 ARG 0.005 0.001 ARG D 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 4) link_NAG-ASN : angle 2.96806 ( 12) link_BETA1-4 : bond 0.00549 ( 2) link_BETA1-4 : angle 1.84005 ( 6) hydrogen bonds : bond 0.03655 ( 91) hydrogen bonds : angle 8.08091 ( 189) SS BOND : bond 0.00250 ( 18) SS BOND : angle 1.79117 ( 36) covalent geometry : bond 0.00319 ( 5925) covalent geometry : angle 0.63067 ( 8010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.5198 (OUTLIER) cc_final: 0.4946 (tp) REVERT: A 126 PHE cc_start: 0.8113 (t80) cc_final: 0.7847 (t80) REVERT: A 128 ASN cc_start: 0.8482 (t0) cc_final: 0.7989 (t0) REVERT: A 275 TYR cc_start: 0.3685 (m-10) cc_final: 0.3470 (m-10) REVERT: A 294 MET cc_start: 0.5391 (tmm) cc_final: 0.4299 (tmm) REVERT: A 300 ARG cc_start: 0.5686 (tpp80) cc_final: 0.5468 (tpp80) REVERT: A 306 GLU cc_start: 0.5567 (OUTLIER) cc_final: 0.5272 (mm-30) REVERT: A 323 ASP cc_start: 0.6937 (p0) cc_final: 0.6728 (p0) REVERT: D 301 MET cc_start: 0.8104 (tpp) cc_final: 0.7904 (tpt) outliers start: 32 outliers final: 13 residues processed: 115 average time/residue: 0.2265 time to fit residues: 33.1290 Evaluate side-chains 94 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 37 optimal weight: 0.0670 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.236117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.186339 restraints weight = 7351.955| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 2.50 r_work: 0.4286 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5949 Z= 0.135 Angle : 0.611 10.211 8064 Z= 0.300 Chirality : 0.048 0.367 896 Planarity : 0.004 0.045 1029 Dihedral : 6.035 42.185 919 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 4.68 % Allowed : 29.80 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.31), residues: 718 helix: 0.70 (1.23), residues: 17 sheet: -2.34 (0.45), residues: 120 loop : -1.18 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 375 HIS 0.003 0.001 HIS D 302 PHE 0.015 0.002 PHE D 371 TYR 0.032 0.002 TYR A 64 ARG 0.006 0.001 ARG A 228 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 4) link_NAG-ASN : angle 2.72915 ( 12) link_BETA1-4 : bond 0.00340 ( 2) link_BETA1-4 : angle 2.11223 ( 6) hydrogen bonds : bond 0.03054 ( 91) hydrogen bonds : angle 7.21082 ( 189) SS BOND : bond 0.00382 ( 18) SS BOND : angle 1.13443 ( 36) covalent geometry : bond 0.00312 ( 5925) covalent geometry : angle 0.59671 ( 8010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.5148 (t) cc_final: 0.4908 (t) REVERT: A 38 LEU cc_start: 0.4093 (OUTLIER) cc_final: 0.3683 (mm) REVERT: A 67 ILE cc_start: 0.5402 (OUTLIER) cc_final: 0.5063 (tp) REVERT: A 126 PHE cc_start: 0.8079 (t80) cc_final: 0.7625 (t80) REVERT: A 294 MET cc_start: 0.5434 (tmm) cc_final: 0.4534 (tmm) REVERT: A 300 ARG cc_start: 0.5689 (tpp80) cc_final: 0.5488 (tpp80) REVERT: A 306 GLU cc_start: 0.5593 (OUTLIER) cc_final: 0.5243 (mm-30) REVERT: A 323 ASP cc_start: 0.6644 (p0) cc_final: 0.6429 (p0) REVERT: A 485 LEU cc_start: 0.6884 (tp) cc_final: 0.6550 (pp) outliers start: 30 outliers final: 15 residues processed: 111 average time/residue: 0.2154 time to fit residues: 31.4249 Evaluate side-chains 97 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 6 optimal weight: 0.0170 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 59 optimal weight: 0.5980 chunk 65 optimal weight: 0.4980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.243270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.200132 restraints weight = 7559.807| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 3.40 r_work: 0.4247 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5949 Z= 0.109 Angle : 0.580 9.045 8064 Z= 0.279 Chirality : 0.047 0.346 896 Planarity : 0.004 0.040 1029 Dihedral : 5.606 41.042 917 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.52 % Allowed : 31.36 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.31), residues: 718 helix: 0.69 (1.22), residues: 17 sheet: -2.44 (0.50), residues: 98 loop : -1.12 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 140 HIS 0.003 0.001 HIS D 302 PHE 0.012 0.001 PHE D 224 TYR 0.017 0.001 TYR A 64 ARG 0.005 0.000 ARG D 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 4) link_NAG-ASN : angle 2.61617 ( 12) link_BETA1-4 : bond 0.00357 ( 2) link_BETA1-4 : angle 1.99546 ( 6) hydrogen bonds : bond 0.02683 ( 91) hydrogen bonds : angle 6.82913 ( 189) SS BOND : bond 0.00214 ( 18) SS BOND : angle 1.04518 ( 36) covalent geometry : bond 0.00249 ( 5925) covalent geometry : angle 0.56578 ( 8010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.5451 (OUTLIER) cc_final: 0.5120 (tp) REVERT: A 287 CYS cc_start: 0.4980 (OUTLIER) cc_final: 0.4312 (t) REVERT: A 294 MET cc_start: 0.5451 (tmm) cc_final: 0.5115 (tmm) REVERT: A 306 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.5211 (mm-30) REVERT: A 323 ASP cc_start: 0.6702 (p0) cc_final: 0.6489 (p0) REVERT: A 485 LEU cc_start: 0.7023 (tp) cc_final: 0.6686 (pp) outliers start: 29 outliers final: 16 residues processed: 112 average time/residue: 0.1953 time to fit residues: 28.2392 Evaluate side-chains 97 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 38 optimal weight: 0.0070 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.4946 r_free = 0.4946 target = 0.241154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.187954 restraints weight = 7549.602| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 2.67 r_work: 0.4255 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5949 Z= 0.147 Angle : 0.595 8.235 8064 Z= 0.288 Chirality : 0.047 0.306 896 Planarity : 0.004 0.072 1029 Dihedral : 5.538 42.272 915 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 5.46 % Allowed : 30.58 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.31), residues: 718 helix: 0.92 (1.23), residues: 17 sheet: -2.42 (0.47), residues: 108 loop : -1.14 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 300 HIS 0.004 0.001 HIS A 346 PHE 0.013 0.001 PHE D 224 TYR 0.014 0.001 TYR A 64 ARG 0.005 0.000 ARG D 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 4) link_NAG-ASN : angle 2.57550 ( 12) link_BETA1-4 : bond 0.00240 ( 2) link_BETA1-4 : angle 1.97173 ( 6) hydrogen bonds : bond 0.02646 ( 91) hydrogen bonds : angle 6.61056 ( 189) SS BOND : bond 0.00294 ( 18) SS BOND : angle 1.00628 ( 36) covalent geometry : bond 0.00344 ( 5925) covalent geometry : angle 0.58215 ( 8010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.5707 (OUTLIER) cc_final: 0.5393 (tp) REVERT: A 69 LEU cc_start: 0.3723 (OUTLIER) cc_final: 0.3431 (pp) REVERT: A 287 CYS cc_start: 0.5127 (OUTLIER) cc_final: 0.4468 (t) REVERT: A 294 MET cc_start: 0.5511 (tmm) cc_final: 0.5001 (tmm) REVERT: A 306 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.5261 (mm-30) REVERT: A 323 ASP cc_start: 0.6624 (p0) cc_final: 0.6410 (p0) REVERT: A 485 LEU cc_start: 0.7099 (tp) cc_final: 0.6751 (pp) REVERT: D 358 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7182 (t) outliers start: 35 outliers final: 20 residues processed: 107 average time/residue: 0.1786 time to fit residues: 25.2473 Evaluate side-chains 99 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 358 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 66 optimal weight: 0.0040 chunk 46 optimal weight: 0.0000 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- 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 = 0.4938 r_free = 0.4938 target = 0.240345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.188135 restraints weight = 7508.324| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 2.56 r_work: 0.4280 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5949 Z= 0.143 Angle : 0.596 7.642 8064 Z= 0.290 Chirality : 0.047 0.294 896 Planarity : 0.004 0.061 1029 Dihedral : 5.549 42.477 915 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.99 % Allowed : 30.73 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.31), residues: 718 helix: 1.08 (1.25), residues: 17 sheet: -2.53 (0.46), residues: 108 loop : -1.18 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 140 HIS 0.004 0.001 HIS D 302 PHE 0.015 0.002 PHE A 126 TYR 0.015 0.001 TYR D 184 ARG 0.005 0.001 ARG D 365 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 4) link_NAG-ASN : angle 2.44342 ( 12) link_BETA1-4 : bond 0.00241 ( 2) link_BETA1-4 : angle 1.92175 ( 6) hydrogen bonds : bond 0.02615 ( 91) hydrogen bonds : angle 6.48447 ( 189) SS BOND : bond 0.00260 ( 18) SS BOND : angle 1.01959 ( 36) covalent geometry : bond 0.00333 ( 5925) covalent geometry : angle 0.58451 ( 8010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.5760 (OUTLIER) cc_final: 0.5458 (tp) REVERT: A 69 LEU cc_start: 0.3722 (OUTLIER) cc_final: 0.3446 (pp) REVERT: A 126 PHE cc_start: 0.8102 (t80) cc_final: 0.7570 (t80) REVERT: A 287 CYS cc_start: 0.5045 (OUTLIER) cc_final: 0.4359 (t) REVERT: A 294 MET cc_start: 0.5508 (tmm) cc_final: 0.4884 (tmm) REVERT: A 306 GLU cc_start: 0.5602 (OUTLIER) cc_final: 0.5274 (mm-30) REVERT: A 485 LEU cc_start: 0.7076 (tp) cc_final: 0.6801 (pp) REVERT: D 358 THR cc_start: 0.7620 (OUTLIER) cc_final: 0.7220 (t) outliers start: 32 outliers final: 21 residues processed: 104 average time/residue: 0.2145 time to fit residues: 29.4321 Evaluate side-chains 99 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 358 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 51 optimal weight: 0.0570 chunk 28 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.240333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.199363 restraints weight = 7563.764| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 3.57 r_work: 0.4184 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5949 Z= 0.138 Angle : 0.594 7.400 8064 Z= 0.290 Chirality : 0.047 0.284 896 Planarity : 0.004 0.056 1029 Dihedral : 5.584 42.347 915 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 5.30 % Allowed : 30.89 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.31), residues: 718 helix: 1.58 (1.26), residues: 16 sheet: -2.58 (0.45), residues: 108 loop : -1.15 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 140 HIS 0.005 0.001 HIS A 346 PHE 0.017 0.001 PHE D 224 TYR 0.017 0.002 TYR D 184 ARG 0.005 0.001 ARG D 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 4) link_NAG-ASN : angle 2.40132 ( 12) link_BETA1-4 : bond 0.00259 ( 2) link_BETA1-4 : angle 1.76231 ( 6) hydrogen bonds : bond 0.02658 ( 91) hydrogen bonds : angle 6.43289 ( 189) SS BOND : bond 0.00255 ( 18) SS BOND : angle 0.95289 ( 36) covalent geometry : bond 0.00322 ( 5925) covalent geometry : angle 0.58372 ( 8010) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.4488 (OUTLIER) cc_final: 0.4141 (mm) REVERT: A 67 ILE cc_start: 0.5967 (OUTLIER) cc_final: 0.5695 (tp) REVERT: A 69 LEU cc_start: 0.3865 (OUTLIER) cc_final: 0.3577 (pp) REVERT: A 126 PHE cc_start: 0.8179 (t80) cc_final: 0.7824 (t80) REVERT: A 287 CYS cc_start: 0.5154 (OUTLIER) cc_final: 0.4416 (t) REVERT: A 294 MET cc_start: 0.5518 (tmm) cc_final: 0.4837 (tmm) REVERT: A 306 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.5296 (mm-30) REVERT: A 485 LEU cc_start: 0.7125 (tp) cc_final: 0.6860 (pp) REVERT: D 358 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7287 (t) outliers start: 34 outliers final: 21 residues processed: 102 average time/residue: 0.1873 time to fit residues: 24.9698 Evaluate side-chains 99 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 358 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.0020 chunk 40 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 46 optimal weight: 0.0040 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.241238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.200022 restraints weight = 7471.361| |-----------------------------------------------------------------------------| r_work (start): 0.4593 rms_B_bonded: 3.67 r_work: 0.4181 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5949 Z= 0.119 Angle : 0.588 8.208 8064 Z= 0.285 Chirality : 0.046 0.290 896 Planarity : 0.004 0.054 1029 Dihedral : 5.500 41.430 915 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 5.15 % Allowed : 30.89 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.31), residues: 718 helix: 1.30 (1.28), residues: 17 sheet: -2.59 (0.45), residues: 108 loop : -1.15 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 140 HIS 0.003 0.001 HIS D 302 PHE 0.014 0.001 PHE D 224 TYR 0.015 0.001 TYR D 184 ARG 0.005 0.000 ARG D 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 4) link_NAG-ASN : angle 2.39357 ( 12) link_BETA1-4 : bond 0.00281 ( 2) link_BETA1-4 : angle 1.80889 ( 6) hydrogen bonds : bond 0.02516 ( 91) hydrogen bonds : angle 6.30555 ( 189) SS BOND : bond 0.00210 ( 18) SS BOND : angle 0.92058 ( 36) covalent geometry : bond 0.00276 ( 5925) covalent geometry : angle 0.57737 ( 8010) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.4417 (OUTLIER) cc_final: 0.4190 (mm) REVERT: A 67 ILE cc_start: 0.5958 (OUTLIER) cc_final: 0.5691 (tp) REVERT: A 69 LEU cc_start: 0.3869 (OUTLIER) cc_final: 0.3579 (pp) REVERT: A 126 PHE cc_start: 0.8080 (t80) cc_final: 0.7694 (t80) REVERT: A 128 ASN cc_start: 0.8475 (t0) cc_final: 0.7999 (t0) REVERT: A 287 CYS cc_start: 0.5163 (OUTLIER) cc_final: 0.4408 (t) REVERT: A 294 MET cc_start: 0.5496 (tmm) cc_final: 0.4871 (tmm) REVERT: A 306 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5242 (mm-30) REVERT: A 485 LEU cc_start: 0.7103 (tp) cc_final: 0.6862 (pp) REVERT: D 358 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7276 (t) outliers start: 33 outliers final: 21 residues processed: 104 average time/residue: 0.1900 time to fit residues: 25.7419 Evaluate side-chains 100 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 358 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 59 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 346 HIS A 554 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.237241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.195545 restraints weight = 7531.478| |-----------------------------------------------------------------------------| r_work (start): 0.4564 rms_B_bonded: 3.47 r_work: 0.4168 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5949 Z= 0.191 Angle : 0.648 8.639 8064 Z= 0.317 Chirality : 0.048 0.279 896 Planarity : 0.004 0.051 1029 Dihedral : 5.749 43.452 915 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 4.68 % Allowed : 31.83 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.31), residues: 718 helix: 0.24 (1.19), residues: 17 sheet: -2.63 (0.44), residues: 118 loop : -1.20 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 140 HIS 0.005 0.001 HIS D 302 PHE 0.015 0.002 PHE D 224 TYR 0.020 0.002 TYR D 184 ARG 0.009 0.001 ARG D 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 4) link_NAG-ASN : angle 2.42563 ( 12) link_BETA1-4 : bond 0.00285 ( 2) link_BETA1-4 : angle 1.87006 ( 6) hydrogen bonds : bond 0.02872 ( 91) hydrogen bonds : angle 6.45077 ( 189) SS BOND : bond 0.00354 ( 18) SS BOND : angle 1.10611 ( 36) covalent geometry : bond 0.00450 ( 5925) covalent geometry : angle 0.63669 ( 8010) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.4680 (OUTLIER) cc_final: 0.4425 (mm) REVERT: A 67 ILE cc_start: 0.6040 (OUTLIER) cc_final: 0.5740 (tp) REVERT: A 126 PHE cc_start: 0.8105 (t80) cc_final: 0.7783 (t80) REVERT: A 128 ASN cc_start: 0.8452 (t0) cc_final: 0.8006 (t0) REVERT: A 287 CYS cc_start: 0.5173 (OUTLIER) cc_final: 0.4413 (t) REVERT: A 294 MET cc_start: 0.5552 (tmm) cc_final: 0.5324 (tmm) REVERT: A 485 LEU cc_start: 0.7162 (tp) cc_final: 0.6906 (pp) REVERT: D 209 LYS cc_start: 0.6786 (mmmt) cc_final: 0.5930 (mttp) REVERT: D 358 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7317 (t) outliers start: 30 outliers final: 19 residues processed: 101 average time/residue: 0.1804 time to fit residues: 23.9198 Evaluate side-chains 95 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 0.3980 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.232891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.178434 restraints weight = 7497.651| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.72 r_work: 0.4185 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 5949 Z= 0.253 Angle : 0.724 9.752 8064 Z= 0.358 Chirality : 0.050 0.273 896 Planarity : 0.005 0.059 1029 Dihedral : 6.224 45.879 915 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 4.52 % Allowed : 32.29 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.31), residues: 718 helix: 0.93 (1.24), residues: 18 sheet: -2.82 (0.44), residues: 112 loop : -1.31 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 140 HIS 0.008 0.001 HIS D 302 PHE 0.017 0.002 PHE D 224 TYR 0.027 0.002 TYR D 184 ARG 0.008 0.001 ARG D 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 4) link_NAG-ASN : angle 2.51733 ( 12) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.85234 ( 6) hydrogen bonds : bond 0.03002 ( 91) hydrogen bonds : angle 6.60243 ( 189) SS BOND : bond 0.00465 ( 18) SS BOND : angle 1.38986 ( 36) covalent geometry : bond 0.00596 ( 5925) covalent geometry : angle 0.71167 ( 8010) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.4845 (OUTLIER) cc_final: 0.4464 (mm) REVERT: A 69 LEU cc_start: 0.4022 (OUTLIER) cc_final: 0.3747 (pp) REVERT: A 126 PHE cc_start: 0.8091 (t80) cc_final: 0.7719 (t80) REVERT: A 128 ASN cc_start: 0.8453 (t0) cc_final: 0.8010 (t0) REVERT: A 176 TRP cc_start: 0.7645 (OUTLIER) cc_final: 0.6019 (t60) REVERT: A 287 CYS cc_start: 0.5228 (OUTLIER) cc_final: 0.4440 (t) REVERT: A 294 MET cc_start: 0.5603 (tmm) cc_final: 0.5338 (tmm) REVERT: D 209 LYS cc_start: 0.6759 (mmmt) cc_final: 0.5998 (mttp) outliers start: 29 outliers final: 22 residues processed: 102 average time/residue: 0.1827 time to fit residues: 24.5554 Evaluate side-chains 99 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 357 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 26 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.237215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.190633 restraints weight = 7541.861| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 2.87 r_work: 0.4255 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5949 Z= 0.140 Angle : 0.646 9.402 8064 Z= 0.316 Chirality : 0.048 0.284 896 Planarity : 0.005 0.060 1029 Dihedral : 5.809 42.309 915 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 3.90 % Allowed : 33.07 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.31), residues: 718 helix: 0.91 (1.27), residues: 18 sheet: -2.65 (0.45), residues: 118 loop : -1.23 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 140 HIS 0.003 0.001 HIS D 302 PHE 0.016 0.001 PHE D 224 TYR 0.018 0.002 TYR D 184 ARG 0.009 0.001 ARG D 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 4) link_NAG-ASN : angle 2.46013 ( 12) link_BETA1-4 : bond 0.00173 ( 2) link_BETA1-4 : angle 1.90721 ( 6) hydrogen bonds : bond 0.02694 ( 91) hydrogen bonds : angle 6.41230 ( 189) SS BOND : bond 0.00265 ( 18) SS BOND : angle 1.19490 ( 36) covalent geometry : bond 0.00329 ( 5925) covalent geometry : angle 0.63393 ( 8010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4042.84 seconds wall clock time: 71 minutes 51.95 seconds (4311.95 seconds total)