Starting phenix.real_space_refine on Tue Mar 3 12:59:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uae_26422/03_2026/7uae_26422.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uae_26422/03_2026/7uae_26422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uae_26422/03_2026/7uae_26422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uae_26422/03_2026/7uae_26422.map" model { file = "/net/cci-nas-00/data/ceres_data/7uae_26422/03_2026/7uae_26422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uae_26422/03_2026/7uae_26422.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 S 21 5.16 5 C 2834 2.51 5 N 748 2.21 5 O 907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4513 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4313 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" 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: "E" 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: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.00, per 1000 atoms: 0.22 Number of scatterers: 4513 At special positions: 0 Unit cell: (99.64, 81.62, 92.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 21 16.00 O 907 8.00 N 748 7.00 C 2834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 431 " distance=2.04 Simple disulfide: pdb=" SG CYS A 557 " - pdb=" SG CYS A 559 " distance=2.05 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 B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG F 1 " - " FUC F 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 704 " - " ASN A 539 " " NAG B 1 " - " ASN A 140 " " NAG C 1 " - " ASN A 258 " " NAG D 1 " - " ASN A 222 " " NAG E 1 " - " ASN A 440 " " NAG F 1 " - " ASN A 414 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 258.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 165 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 155 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 159 " 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 998 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 10 sheets defined 23.6% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 440 through 448 removed outlier: 4.317A pdb=" N GLU A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 516 through 520 Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 597 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112 removed outlier: 7.977A pdb=" N PHE A 122 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 82 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 121 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 269 removed outlier: 5.726A pdb=" N LEU A 421 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS A 349 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP A 423 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE A 347 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 281 removed outlier: 6.790A pdb=" N LEU A 358 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR A 379 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 360 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 434 through 438 Processing sheet with id=AA8, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AA9, first strand: chain 'A' and resid 454 through 455 removed outlier: 3.951A pdb=" N GLY A 466 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 482 " --> pdb=" O GLY A 569 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 552 through 553 158 hydrogen bonds defined for protein. 354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1084 1.33 - 1.45: 1057 1.45 - 1.57: 2449 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 4620 Sorted by residual: bond pdb=" CZ ARG A 169 " pdb=" NH2 ARG A 169 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG A 172 " pdb=" NH2 ARG A 172 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.92e+00 bond pdb=" N VAL A 371 " pdb=" CA VAL A 371 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.71e+00 bond pdb=" CZ ARG A 518 " pdb=" NH2 ARG A 518 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.58e+00 bond pdb=" CZ ARG A 103 " pdb=" NH2 ARG A 103 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.47e+00 ... (remaining 4615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 4427 1.81 - 3.61: 1580 3.61 - 5.42: 247 5.42 - 7.22: 15 7.22 - 9.03: 2 Bond angle restraints: 6271 Sorted by residual: angle pdb=" CA PHE A 590 " pdb=" CB PHE A 590 " pdb=" CG PHE A 590 " ideal model delta sigma weight residual 113.80 118.92 -5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" CA ASP A 564 " pdb=" CB ASP A 564 " pdb=" CG ASP A 564 " ideal model delta sigma weight residual 112.60 117.67 -5.07 1.00e+00 1.00e+00 2.57e+01 angle pdb=" N TYR A 113 " pdb=" CA TYR A 113 " pdb=" C TYR A 113 " ideal model delta sigma weight residual 111.07 116.26 -5.19 1.07e+00 8.73e-01 2.35e+01 angle pdb=" CB HIS A 573 " pdb=" CG HIS A 573 " pdb=" CD2 HIS A 573 " ideal model delta sigma weight residual 131.20 124.97 6.23 1.30e+00 5.92e-01 2.30e+01 angle pdb=" OE1 GLN A 345 " pdb=" CD GLN A 345 " pdb=" NE2 GLN A 345 " ideal model delta sigma weight residual 122.60 117.87 4.73 1.00e+00 1.00e+00 2.23e+01 ... (remaining 6266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 2740 21.24 - 42.48: 119 42.48 - 63.72: 19 63.72 - 84.96: 23 84.96 - 106.19: 13 Dihedral angle restraints: 2914 sinusoidal: 1359 harmonic: 1555 Sorted by residual: dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual 93.00 -176.94 -90.06 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS A 557 " pdb=" SG CYS A 557 " pdb=" SG CYS A 559 " pdb=" CB CYS A 559 " ideal model delta sinusoidal sigma weight residual -86.00 -139.17 53.17 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CA TRP A 567 " pdb=" C TRP A 567 " pdb=" N SER A 568 " pdb=" CA SER A 568 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 2911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 398 0.079 - 0.157: 236 0.157 - 0.236: 62 0.236 - 0.314: 14 0.314 - 0.393: 4 Chirality restraints: 714 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.93e+02 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.44e+01 chirality pdb=" C1 FUC F 4 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 4 " pdb=" O5 FUC F 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.73e+01 ... (remaining 711 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.314 2.00e-02 2.50e+03 2.72e-01 9.25e+02 pdb=" C7 NAG C 1 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.474 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.205 2.00e-02 2.50e+03 1.68e-01 3.55e+02 pdb=" C7 NAG D 1 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.273 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " 0.183 2.00e-02 2.50e+03 1.51e-01 2.85e+02 pdb=" C7 NAG A 704 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " -0.245 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " -0.021 2.00e-02 2.50e+03 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 823 2.81 - 3.33: 4208 3.33 - 3.85: 7306 3.85 - 4.38: 9238 4.38 - 4.90: 15059 Nonbonded interactions: 36634 Sorted by model distance: nonbonded pdb=" OD1 ASP A 288 " pdb="CA CA A 701 " model vdw 2.282 2.510 nonbonded pdb=" OE2 GLU A 272 " pdb="CA CA A 703 " model vdw 2.302 2.510 nonbonded pdb=" O TYR A 313 " pdb="CA CA A 703 " model vdw 2.329 2.510 nonbonded pdb=" OD1 ASP A 285 " pdb="CA CA A 701 " model vdw 2.329 2.510 nonbonded pdb=" OD2 ASP A 285 " pdb="CA CA A 701 " model vdw 2.379 2.510 ... (remaining 36629 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' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 0.660 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 6.260 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.016 0.485 4643 Z= 0.796 Angle : 1.763 9.028 6326 Z= 1.169 Chirality : 0.102 0.393 714 Planarity : 0.020 0.272 797 Dihedral : 16.442 106.193 1901 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.34), residues: 533 helix: -0.97 (0.58), residues: 62 sheet: 0.51 (0.43), residues: 131 loop : -0.13 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 252 TYR 0.104 0.020 TYR A 313 PHE 0.067 0.011 PHE A 593 TRP 0.071 0.016 TRP A 544 HIS 0.012 0.003 HIS A 573 Details of bonding type rmsd covalent geometry : bond 0.01154 ( 4620) covalent geometry : angle 1.75644 ( 6271) SS BOND : bond 0.00893 ( 5) SS BOND : angle 2.72348 ( 10) hydrogen bonds : bond 0.18065 ( 152) hydrogen bonds : angle 7.43262 ( 354) metal coordination : bond 0.46237 ( 3) link_BETA1-4 : bond 0.00170 ( 8) link_BETA1-4 : angle 1.57309 ( 24) link_BETA1-6 : bond 0.00548 ( 1) link_BETA1-6 : angle 2.65351 ( 3) link_NAG-ASN : bond 0.00600 ( 6) link_NAG-ASN : angle 3.08084 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.6218 (p) cc_final: 0.5910 (p) REVERT: A 207 ASP cc_start: 0.7669 (t0) cc_final: 0.7190 (t0) REVERT: A 212 MET cc_start: 0.8801 (mmm) cc_final: 0.8480 (mmm) REVERT: A 251 GLU cc_start: 0.7569 (tt0) cc_final: 0.7321 (tt0) REVERT: A 272 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7292 (mp0) REVERT: A 423 ASP cc_start: 0.7931 (m-30) cc_final: 0.7572 (m-30) REVERT: A 447 ASN cc_start: 0.8660 (m-40) cc_final: 0.8232 (m-40) REVERT: A 512 ASP cc_start: 0.8064 (t0) cc_final: 0.7856 (t0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.6071 time to fit residues: 73.9972 Evaluate side-chains 79 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.0060 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 461 ASN A 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.085460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.075513 restraints weight = 7918.032| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.27 r_work: 0.3020 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4643 Z= 0.146 Angle : 0.698 9.856 6326 Z= 0.355 Chirality : 0.047 0.210 714 Planarity : 0.004 0.025 797 Dihedral : 11.443 64.246 890 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.68 % Allowed : 10.29 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.34), residues: 533 helix: 0.04 (0.63), residues: 66 sheet: 0.37 (0.43), residues: 137 loop : -0.01 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 549 TYR 0.011 0.001 TYR A 97 PHE 0.016 0.001 PHE A 245 TRP 0.010 0.001 TRP A 361 HIS 0.009 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4620) covalent geometry : angle 0.67497 ( 6271) SS BOND : bond 0.01668 ( 5) SS BOND : angle 1.49369 ( 10) hydrogen bonds : bond 0.04298 ( 152) hydrogen bonds : angle 5.97877 ( 354) metal coordination : bond 0.02113 ( 3) link_BETA1-4 : bond 0.00419 ( 8) link_BETA1-4 : angle 1.85136 ( 24) link_BETA1-6 : bond 0.00288 ( 1) link_BETA1-6 : angle 2.07211 ( 3) link_NAG-ASN : bond 0.00299 ( 6) link_NAG-ASN : angle 2.44203 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 207 ASP cc_start: 0.8286 (t0) cc_final: 0.7942 (t0) REVERT: A 397 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7733 (mm-30) REVERT: A 411 ASP cc_start: 0.8222 (t0) cc_final: 0.7885 (t0) REVERT: A 423 ASP cc_start: 0.8547 (m-30) cc_final: 0.8266 (m-30) REVERT: A 492 GLU cc_start: 0.6672 (tp30) cc_final: 0.5692 (tm-30) REVERT: A 494 ASP cc_start: 0.8518 (m-30) cc_final: 0.8253 (m-30) REVERT: A 512 ASP cc_start: 0.8510 (t0) cc_final: 0.8251 (t0) outliers start: 8 outliers final: 3 residues processed: 87 average time/residue: 0.5662 time to fit residues: 51.0774 Evaluate side-chains 78 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 398 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 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 = 0.3316 r_free = 0.3316 target = 0.085163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.075411 restraints weight = 7897.040| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.26 r_work: 0.3039 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4643 Z= 0.140 Angle : 0.624 9.404 6326 Z= 0.315 Chirality : 0.046 0.200 714 Planarity : 0.003 0.029 797 Dihedral : 7.355 35.667 890 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.68 % Allowed : 13.66 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.35), residues: 533 helix: 0.18 (0.64), residues: 69 sheet: 0.39 (0.41), residues: 148 loop : 0.03 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.016 0.001 TYR A 97 PHE 0.011 0.001 PHE A 593 TRP 0.009 0.001 TRP A 361 HIS 0.008 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4620) covalent geometry : angle 0.60136 ( 6271) SS BOND : bond 0.00718 ( 5) SS BOND : angle 1.11580 ( 10) hydrogen bonds : bond 0.03829 ( 152) hydrogen bonds : angle 5.49848 ( 354) metal coordination : bond 0.00401 ( 3) link_BETA1-4 : bond 0.00375 ( 8) link_BETA1-4 : angle 1.96492 ( 24) link_BETA1-6 : bond 0.00367 ( 1) link_BETA1-6 : angle 1.90784 ( 3) link_NAG-ASN : bond 0.00238 ( 6) link_NAG-ASN : angle 2.14080 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8781 (tp30) cc_final: 0.8534 (tp30) REVERT: A 207 ASP cc_start: 0.8283 (t0) cc_final: 0.7920 (t0) REVERT: A 251 GLU cc_start: 0.8713 (tt0) cc_final: 0.8481 (tt0) REVERT: A 397 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7747 (mm-30) REVERT: A 411 ASP cc_start: 0.8431 (t0) cc_final: 0.7987 (t0) REVERT: A 423 ASP cc_start: 0.8508 (m-30) cc_final: 0.8232 (m-30) REVERT: A 492 GLU cc_start: 0.6727 (tp30) cc_final: 0.6462 (tm-30) REVERT: A 494 ASP cc_start: 0.8516 (m-30) cc_final: 0.8238 (m-30) REVERT: A 512 ASP cc_start: 0.8518 (t0) cc_final: 0.8278 (t0) REVERT: A 521 MET cc_start: 0.8977 (mtp) cc_final: 0.8774 (mtm) REVERT: A 525 MET cc_start: 0.9079 (mmm) cc_final: 0.8682 (mtm) REVERT: A 585 ASP cc_start: 0.8405 (t70) cc_final: 0.7797 (t0) REVERT: A 594 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7723 (mm-30) outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 0.5356 time to fit residues: 46.7322 Evaluate side-chains 79 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 387 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.073992 restraints weight = 7992.233| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.26 r_work: 0.2997 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4643 Z= 0.219 Angle : 0.643 10.198 6326 Z= 0.328 Chirality : 0.047 0.204 714 Planarity : 0.004 0.030 797 Dihedral : 5.667 32.218 890 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.10 % Allowed : 14.29 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.35), residues: 533 helix: 0.31 (0.64), residues: 69 sheet: 0.43 (0.42), residues: 145 loop : -0.13 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 578 TYR 0.017 0.002 TYR A 97 PHE 0.012 0.002 PHE A 486 TRP 0.010 0.001 TRP A 361 HIS 0.008 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 4620) covalent geometry : angle 0.61740 ( 6271) SS BOND : bond 0.00305 ( 5) SS BOND : angle 1.90261 ( 10) hydrogen bonds : bond 0.03960 ( 152) hydrogen bonds : angle 5.52847 ( 354) metal coordination : bond 0.00701 ( 3) link_BETA1-4 : bond 0.00298 ( 8) link_BETA1-4 : angle 1.92024 ( 24) link_BETA1-6 : bond 0.00214 ( 1) link_BETA1-6 : angle 2.41840 ( 3) link_NAG-ASN : bond 0.00348 ( 6) link_NAG-ASN : angle 2.09784 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8807 (tp30) cc_final: 0.8535 (tp30) REVERT: A 196 ASP cc_start: 0.8717 (p0) cc_final: 0.8487 (p0) REVERT: A 207 ASP cc_start: 0.8286 (t0) cc_final: 0.7909 (t0) REVERT: A 227 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8708 (p) REVERT: A 251 GLU cc_start: 0.8711 (tt0) cc_final: 0.8462 (tt0) REVERT: A 397 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7689 (mm-30) REVERT: A 411 ASP cc_start: 0.8463 (t0) cc_final: 0.8002 (t0) REVERT: A 423 ASP cc_start: 0.8508 (m-30) cc_final: 0.8248 (m-30) REVERT: A 492 GLU cc_start: 0.6809 (tp30) cc_final: 0.6475 (tm-30) REVERT: A 494 ASP cc_start: 0.8494 (m-30) cc_final: 0.8251 (m-30) REVERT: A 512 ASP cc_start: 0.8512 (t0) cc_final: 0.8292 (t0) REVERT: A 521 MET cc_start: 0.8972 (mtp) cc_final: 0.8766 (mtm) REVERT: A 525 MET cc_start: 0.9059 (mmm) cc_final: 0.8660 (mtm) REVERT: A 585 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7877 (t0) outliers start: 10 outliers final: 5 residues processed: 81 average time/residue: 0.4768 time to fit residues: 40.1996 Evaluate side-chains 77 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 585 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 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 392 HIS A 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.075230 restraints weight = 7857.544| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.24 r_work: 0.3021 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4643 Z= 0.148 Angle : 0.597 10.370 6326 Z= 0.306 Chirality : 0.045 0.210 714 Planarity : 0.003 0.028 797 Dihedral : 5.081 32.666 890 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.47 % Allowed : 16.18 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.35), residues: 533 helix: 0.65 (0.65), residues: 66 sheet: 0.36 (0.43), residues: 147 loop : -0.17 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 578 TYR 0.018 0.001 TYR A 97 PHE 0.012 0.001 PHE A 527 TRP 0.008 0.001 TRP A 361 HIS 0.007 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4620) covalent geometry : angle 0.57881 ( 6271) SS BOND : bond 0.00215 ( 5) SS BOND : angle 1.34675 ( 10) hydrogen bonds : bond 0.03506 ( 152) hydrogen bonds : angle 5.33947 ( 354) metal coordination : bond 0.00411 ( 3) link_BETA1-4 : bond 0.00375 ( 8) link_BETA1-4 : angle 1.57977 ( 24) link_BETA1-6 : bond 0.00493 ( 1) link_BETA1-6 : angle 1.90253 ( 3) link_NAG-ASN : bond 0.00177 ( 6) link_NAG-ASN : angle 1.93649 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8825 (tp30) cc_final: 0.8546 (tp30) REVERT: A 201 ASP cc_start: 0.8481 (p0) cc_final: 0.8268 (p0) REVERT: A 207 ASP cc_start: 0.8261 (t0) cc_final: 0.7895 (t0) REVERT: A 251 GLU cc_start: 0.8717 (tt0) cc_final: 0.8470 (tt0) REVERT: A 397 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7737 (mm-30) REVERT: A 411 ASP cc_start: 0.8497 (t0) cc_final: 0.7998 (t0) REVERT: A 423 ASP cc_start: 0.8497 (m-30) cc_final: 0.8218 (m-30) REVERT: A 492 GLU cc_start: 0.6819 (tp30) cc_final: 0.6614 (tm-30) REVERT: A 494 ASP cc_start: 0.8486 (m-30) cc_final: 0.8211 (m-30) REVERT: A 512 ASP cc_start: 0.8485 (t0) cc_final: 0.8217 (t0) REVERT: A 525 MET cc_start: 0.9061 (mmm) cc_final: 0.8678 (mtm) REVERT: A 585 ASP cc_start: 0.8397 (t70) cc_final: 0.7857 (t0) outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 0.5008 time to fit residues: 40.1783 Evaluate side-chains 75 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075523 restraints weight = 8059.719| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.29 r_work: 0.3024 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4643 Z= 0.127 Angle : 0.576 10.786 6326 Z= 0.294 Chirality : 0.044 0.215 714 Planarity : 0.003 0.028 797 Dihedral : 4.887 33.583 890 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.52 % Allowed : 15.55 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.36), residues: 533 helix: 0.78 (0.66), residues: 66 sheet: 0.39 (0.43), residues: 149 loop : -0.15 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 579 TYR 0.019 0.001 TYR A 97 PHE 0.012 0.001 PHE A 527 TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4620) covalent geometry : angle 0.55812 ( 6271) SS BOND : bond 0.00189 ( 5) SS BOND : angle 1.08779 ( 10) hydrogen bonds : bond 0.03363 ( 152) hydrogen bonds : angle 5.27779 ( 354) metal coordination : bond 0.00318 ( 3) link_BETA1-4 : bond 0.00396 ( 8) link_BETA1-4 : angle 1.51692 ( 24) link_BETA1-6 : bond 0.00510 ( 1) link_BETA1-6 : angle 1.82492 ( 3) link_NAG-ASN : bond 0.00151 ( 6) link_NAG-ASN : angle 1.90013 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8850 (tp30) cc_final: 0.8564 (tp30) REVERT: A 201 ASP cc_start: 0.8503 (p0) cc_final: 0.8279 (p0) REVERT: A 207 ASP cc_start: 0.8284 (t0) cc_final: 0.7903 (t0) REVERT: A 251 GLU cc_start: 0.8730 (tt0) cc_final: 0.8490 (tt0) REVERT: A 397 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 411 ASP cc_start: 0.8452 (t0) cc_final: 0.7962 (t0) REVERT: A 423 ASP cc_start: 0.8505 (m-30) cc_final: 0.8226 (m-30) REVERT: A 492 GLU cc_start: 0.6825 (tp30) cc_final: 0.6528 (tm-30) REVERT: A 494 ASP cc_start: 0.8475 (m-30) cc_final: 0.8198 (m-30) REVERT: A 512 ASP cc_start: 0.8512 (t0) cc_final: 0.8232 (t0) REVERT: A 525 MET cc_start: 0.9058 (mmm) cc_final: 0.8689 (mtm) REVERT: A 585 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7845 (t0) outliers start: 12 outliers final: 5 residues processed: 85 average time/residue: 0.4753 time to fit residues: 42.0337 Evaluate side-chains 81 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 585 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 34 optimal weight: 0.0370 chunk 23 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 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 = 0.3326 r_free = 0.3326 target = 0.085623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.075945 restraints weight = 7934.500| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.27 r_work: 0.3034 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4643 Z= 0.117 Angle : 0.572 10.996 6326 Z= 0.293 Chirality : 0.045 0.217 714 Planarity : 0.003 0.029 797 Dihedral : 4.700 34.110 890 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.89 % Allowed : 17.44 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.36), residues: 533 helix: 0.93 (0.67), residues: 66 sheet: 0.53 (0.44), residues: 149 loop : -0.11 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 578 TYR 0.007 0.001 TYR A 81 PHE 0.012 0.001 PHE A 527 TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4620) covalent geometry : angle 0.55580 ( 6271) SS BOND : bond 0.00196 ( 5) SS BOND : angle 0.98570 ( 10) hydrogen bonds : bond 0.03233 ( 152) hydrogen bonds : angle 5.19856 ( 354) metal coordination : bond 0.00264 ( 3) link_BETA1-4 : bond 0.00407 ( 8) link_BETA1-4 : angle 1.44172 ( 24) link_BETA1-6 : bond 0.00543 ( 1) link_BETA1-6 : angle 1.73285 ( 3) link_NAG-ASN : bond 0.00116 ( 6) link_NAG-ASN : angle 1.85098 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8514 (p0) cc_final: 0.8282 (p0) REVERT: A 207 ASP cc_start: 0.8239 (t0) cc_final: 0.7865 (t0) REVERT: A 251 GLU cc_start: 0.8727 (tt0) cc_final: 0.8478 (tt0) REVERT: A 397 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7650 (mm-30) REVERT: A 411 ASP cc_start: 0.8458 (t0) cc_final: 0.8004 (t0) REVERT: A 423 ASP cc_start: 0.8498 (m-30) cc_final: 0.8213 (m-30) REVERT: A 492 GLU cc_start: 0.6708 (tp30) cc_final: 0.6386 (tm-30) REVERT: A 494 ASP cc_start: 0.8438 (m-30) cc_final: 0.8172 (m-30) REVERT: A 501 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8067 (t) REVERT: A 512 ASP cc_start: 0.8488 (t0) cc_final: 0.8244 (t0) REVERT: A 525 MET cc_start: 0.9031 (mmm) cc_final: 0.8689 (mtm) REVERT: A 585 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.7872 (t0) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.5089 time to fit residues: 41.8085 Evaluate side-chains 80 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 585 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 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 = 0.3331 r_free = 0.3331 target = 0.085922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.076242 restraints weight = 7985.843| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.28 r_work: 0.3043 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4643 Z= 0.117 Angle : 0.599 11.094 6326 Z= 0.305 Chirality : 0.045 0.250 714 Planarity : 0.003 0.027 797 Dihedral : 4.638 34.499 890 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.10 % Allowed : 17.44 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.36), residues: 533 helix: 0.60 (0.64), residues: 72 sheet: 0.67 (0.45), residues: 148 loop : -0.17 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 372 TYR 0.022 0.001 TYR A 97 PHE 0.012 0.001 PHE A 527 TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4620) covalent geometry : angle 0.58390 ( 6271) SS BOND : bond 0.00148 ( 5) SS BOND : angle 1.09135 ( 10) hydrogen bonds : bond 0.03197 ( 152) hydrogen bonds : angle 5.16870 ( 354) metal coordination : bond 0.00221 ( 3) link_BETA1-4 : bond 0.00412 ( 8) link_BETA1-4 : angle 1.41709 ( 24) link_BETA1-6 : bond 0.00560 ( 1) link_BETA1-6 : angle 1.69040 ( 3) link_NAG-ASN : bond 0.00093 ( 6) link_NAG-ASN : angle 1.84610 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8508 (p0) cc_final: 0.8271 (p0) REVERT: A 207 ASP cc_start: 0.8253 (t0) cc_final: 0.7885 (t0) REVERT: A 251 GLU cc_start: 0.8725 (tt0) cc_final: 0.8474 (tt0) REVERT: A 284 ARG cc_start: 0.4975 (ttt180) cc_final: 0.1905 (tmt170) REVERT: A 397 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 408 THR cc_start: 0.8781 (m) cc_final: 0.8478 (p) REVERT: A 411 ASP cc_start: 0.8457 (t0) cc_final: 0.8007 (t0) REVERT: A 423 ASP cc_start: 0.8505 (m-30) cc_final: 0.8218 (m-30) REVERT: A 492 GLU cc_start: 0.6690 (tp30) cc_final: 0.6430 (tm-30) REVERT: A 494 ASP cc_start: 0.8431 (m-30) cc_final: 0.8196 (m-30) REVERT: A 501 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8043 (t) REVERT: A 512 ASP cc_start: 0.8491 (t0) cc_final: 0.8237 (t0) REVERT: A 525 MET cc_start: 0.9058 (mmm) cc_final: 0.8738 (mtm) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.4908 time to fit residues: 40.4915 Evaluate side-chains 79 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.0270 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 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 = 0.3332 r_free = 0.3332 target = 0.085946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076233 restraints weight = 7954.147| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.28 r_work: 0.3047 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4643 Z= 0.136 Angle : 0.641 12.241 6326 Z= 0.325 Chirality : 0.047 0.325 714 Planarity : 0.003 0.030 797 Dihedral : 4.687 35.608 890 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.89 % Allowed : 17.02 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.36), residues: 533 helix: 0.64 (0.64), residues: 72 sheet: 0.61 (0.45), residues: 148 loop : -0.19 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 372 TYR 0.011 0.001 TYR A 97 PHE 0.011 0.001 PHE A 486 TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4620) covalent geometry : angle 0.61659 ( 6271) SS BOND : bond 0.00335 ( 5) SS BOND : angle 3.15039 ( 10) hydrogen bonds : bond 0.03293 ( 152) hydrogen bonds : angle 5.17385 ( 354) metal coordination : bond 0.00303 ( 3) link_BETA1-4 : bond 0.00389 ( 8) link_BETA1-4 : angle 1.41676 ( 24) link_BETA1-6 : bond 0.00502 ( 1) link_BETA1-6 : angle 1.80744 ( 3) link_NAG-ASN : bond 0.00101 ( 6) link_NAG-ASN : angle 1.85274 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8506 (p0) cc_final: 0.8268 (p0) REVERT: A 207 ASP cc_start: 0.8270 (t0) cc_final: 0.7895 (t0) REVERT: A 251 GLU cc_start: 0.8748 (tt0) cc_final: 0.8499 (tt0) REVERT: A 259 CYS cc_start: 0.7681 (m) cc_final: 0.7377 (m) REVERT: A 284 ARG cc_start: 0.4976 (ttt180) cc_final: 0.1921 (ppt170) REVERT: A 397 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7615 (mm-30) REVERT: A 408 THR cc_start: 0.8783 (m) cc_final: 0.8480 (p) REVERT: A 411 ASP cc_start: 0.8460 (t0) cc_final: 0.7996 (t0) REVERT: A 423 ASP cc_start: 0.8506 (m-30) cc_final: 0.8219 (m-30) REVERT: A 492 GLU cc_start: 0.6687 (tp30) cc_final: 0.6482 (tm-30) REVERT: A 494 ASP cc_start: 0.8410 (m-30) cc_final: 0.8181 (m-30) REVERT: A 501 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8069 (t) REVERT: A 512 ASP cc_start: 0.8491 (t0) cc_final: 0.8238 (t0) REVERT: A 525 MET cc_start: 0.9047 (mmm) cc_final: 0.8727 (mtm) outliers start: 9 outliers final: 6 residues processed: 85 average time/residue: 0.4546 time to fit residues: 40.4335 Evaluate side-chains 78 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 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 = 0.3323 r_free = 0.3323 target = 0.085426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.075685 restraints weight = 8026.759| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.29 r_work: 0.3035 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 4643 Z= 0.177 Angle : 0.674 14.695 6326 Z= 0.340 Chirality : 0.047 0.283 714 Planarity : 0.003 0.029 797 Dihedral : 4.930 41.472 890 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.89 % Allowed : 18.07 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.37), residues: 533 helix: 1.00 (0.67), residues: 66 sheet: 0.54 (0.46), residues: 148 loop : -0.16 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 561 TYR 0.013 0.001 TYR A 97 PHE 0.011 0.001 PHE A 486 TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 4620) covalent geometry : angle 0.65027 ( 6271) SS BOND : bond 0.00546 ( 5) SS BOND : angle 3.08176 ( 10) hydrogen bonds : bond 0.03449 ( 152) hydrogen bonds : angle 5.20408 ( 354) metal coordination : bond 0.00492 ( 3) link_BETA1-4 : bond 0.00354 ( 8) link_BETA1-4 : angle 1.45400 ( 24) link_BETA1-6 : bond 0.00418 ( 1) link_BETA1-6 : angle 2.07558 ( 3) link_NAG-ASN : bond 0.00152 ( 6) link_NAG-ASN : angle 1.88196 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8511 (p0) cc_final: 0.8272 (p0) REVERT: A 207 ASP cc_start: 0.8290 (t0) cc_final: 0.7919 (t0) REVERT: A 251 GLU cc_start: 0.8730 (tt0) cc_final: 0.8488 (tt0) REVERT: A 284 ARG cc_start: 0.5027 (ttt180) cc_final: 0.1991 (ppt170) REVERT: A 397 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7593 (mm-30) REVERT: A 408 THR cc_start: 0.8809 (m) cc_final: 0.8488 (p) REVERT: A 411 ASP cc_start: 0.8495 (t0) cc_final: 0.7956 (t0) REVERT: A 423 ASP cc_start: 0.8511 (m-30) cc_final: 0.8240 (m-30) REVERT: A 463 GLU cc_start: 0.5567 (tp30) cc_final: 0.5207 (tp30) REVERT: A 494 ASP cc_start: 0.8442 (m-30) cc_final: 0.8202 (m-30) REVERT: A 501 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8112 (t) REVERT: A 512 ASP cc_start: 0.8496 (t0) cc_final: 0.8246 (t0) REVERT: A 525 MET cc_start: 0.9071 (mmm) cc_final: 0.8738 (mtm) outliers start: 9 outliers final: 5 residues processed: 78 average time/residue: 0.4949 time to fit residues: 40.2715 Evaluate side-chains 76 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 557 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.085966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076159 restraints weight = 8083.841| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.30 r_work: 0.3041 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4643 Z= 0.138 Angle : 0.654 12.888 6326 Z= 0.331 Chirality : 0.046 0.215 714 Planarity : 0.003 0.033 797 Dihedral : 4.909 43.680 890 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.89 % Allowed : 18.28 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.37), residues: 533 helix: 1.07 (0.67), residues: 66 sheet: 0.58 (0.46), residues: 148 loop : -0.14 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 561 TYR 0.010 0.001 TYR A 97 PHE 0.011 0.001 PHE A 486 TRP 0.007 0.001 TRP A 361 HIS 0.007 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4620) covalent geometry : angle 0.63299 ( 6271) SS BOND : bond 0.00392 ( 5) SS BOND : angle 2.71412 ( 10) hydrogen bonds : bond 0.03297 ( 152) hydrogen bonds : angle 5.17434 ( 354) metal coordination : bond 0.00308 ( 3) link_BETA1-4 : bond 0.00398 ( 8) link_BETA1-4 : angle 1.40242 ( 24) link_BETA1-6 : bond 0.00563 ( 1) link_BETA1-6 : angle 1.82583 ( 3) link_NAG-ASN : bond 0.00101 ( 6) link_NAG-ASN : angle 1.84921 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1938.10 seconds wall clock time: 33 minutes 38.80 seconds (2018.80 seconds total)