Starting phenix.real_space_refine on Thu Jul 24 00:03:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uae_26422/07_2025/7uae_26422.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uae_26422/07_2025/7uae_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_26422/07_2025/7uae_26422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uae_26422/07_2025/7uae_26422.map" model { file = "/net/cci-nas-00/data/ceres_data/7uae_26422/07_2025/7uae_26422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uae_26422/07_2025/7uae_26422.cif" } resolution = 2.6 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= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.20, per 1000 atoms: 0.71 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: 1.32 Conformation dependent library (CDL) restraints added in 480.0 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: 0.57 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: 1.25 Time building geometry restraints manager: 1.54 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: 0.730 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.600 Find NCS groups from input model: 0.060 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:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.071 0.016 TRP A 544 HIS 0.012 0.003 HIS A 573 PHE 0.067 0.011 PHE A 593 TYR 0.104 0.020 TYR A 313 ARG 0.009 0.001 ARG A 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 6) link_NAG-ASN : angle 3.08084 ( 18) link_BETA1-4 : bond 0.00170 ( 8) link_BETA1-4 : angle 1.57309 ( 24) hydrogen bonds : bond 0.18065 ( 152) hydrogen bonds : angle 7.43262 ( 354) link_BETA1-6 : bond 0.00548 ( 1) link_BETA1-6 : angle 2.65351 ( 3) metal coordination : bond 0.46237 ( 3) SS BOND : bond 0.00893 ( 5) SS BOND : angle 2.72348 ( 10) covalent geometry : bond 0.01154 ( 4620) covalent geometry : angle 1.75644 ( 6271) *********************** 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 : 0.528 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: 0.8479 (mmm) REVERT: A 251 GLU cc_start: 0.7570 (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: 0.7573 (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: 0.7857 (t0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 1.3298 time to fit residues: 162.2977 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 : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.084691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.074830 restraints weight = 7865.761| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.25 r_work: 0.3009 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4643 Z= 0.167 Angle : 0.712 9.773 6326 Z= 0.359 Chirality : 0.047 0.209 714 Planarity : 0.004 0.026 797 Dihedral : 11.105 62.435 890 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.68 % Allowed : 10.92 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.06 (0.34), residues: 533 helix: 0.02 (0.63), residues: 66 sheet: 0.41 (0.43), residues: 137 loop : -0.02 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 289 HIS 0.008 0.001 HIS A 155 PHE 0.016 0.002 PHE A 245 TYR 0.010 0.002 TYR A 175 ARG 0.005 0.001 ARG A 549 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 6) link_NAG-ASN : angle 2.44494 ( 18) link_BETA1-4 : bond 0.00474 ( 8) link_BETA1-4 : angle 1.92445 ( 24) hydrogen bonds : bond 0.04294 ( 152) hydrogen bonds : angle 5.97570 ( 354) link_BETA1-6 : bond 0.00163 ( 1) link_BETA1-6 : angle 2.33002 ( 3) metal coordination : bond 0.02637 ( 3) SS BOND : bond 0.00337 ( 5) SS BOND : angle 1.61702 ( 10) covalent geometry : bond 0.00376 ( 4620) covalent geometry : angle 0.68785 ( 6271) *********************** 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 : 0.653 Fit side-chains revert: symmetry clash REVERT: A 207 ASP cc_start: 0.8290 (t0) cc_final: 0.7936 (t0) REVERT: A 397 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 411 ASP cc_start: 0.8330 (t0) cc_final: 0.7976 (t0) REVERT: A 423 ASP cc_start: 0.8539 (m-30) cc_final: 0.8295 (m-30) REVERT: A 492 GLU cc_start: 0.6671 (tp30) cc_final: 0.5673 (tm-30) REVERT: A 494 ASP cc_start: 0.8525 (m-30) cc_final: 0.8290 (m-30) REVERT: A 512 ASP cc_start: 0.8515 (t0) cc_final: 0.8254 (t0) REVERT: A 585 ASP cc_start: 0.8261 (t0) cc_final: 0.7913 (t0) outliers start: 8 outliers final: 3 residues processed: 87 average time/residue: 1.1991 time to fit residues: 108.4609 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 : 0.483 ------------------------------------------------------------------------------- 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 3 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.0060 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.085274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075501 restraints weight = 7869.923| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.25 r_work: 0.3021 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4643 Z= 0.149 Angle : 0.636 9.548 6326 Z= 0.321 Chirality : 0.046 0.198 714 Planarity : 0.003 0.029 797 Dihedral : 7.549 37.216 890 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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 (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: 0.10 (0.35), residues: 533 helix: 0.15 (0.64), residues: 69 sheet: 0.35 (0.41), residues: 148 loop : 0.01 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 361 HIS 0.008 0.001 HIS A 155 PHE 0.011 0.001 PHE A 486 TYR 0.014 0.001 TYR A 97 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 6) link_NAG-ASN : angle 2.12964 ( 18) link_BETA1-4 : bond 0.00354 ( 8) link_BETA1-4 : angle 1.96395 ( 24) hydrogen bonds : bond 0.03889 ( 152) hydrogen bonds : angle 5.55477 ( 354) link_BETA1-6 : bond 0.00352 ( 1) link_BETA1-6 : angle 2.03091 ( 3) metal coordination : bond 0.00500 ( 3) SS BOND : bond 0.00241 ( 5) SS BOND : angle 1.18509 ( 10) covalent geometry : bond 0.00341 ( 4620) covalent geometry : angle 0.61348 ( 6271) *********************** 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 85 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 207 ASP cc_start: 0.8265 (t0) cc_final: 0.7912 (t0) REVERT: A 251 GLU cc_start: 0.8699 (tt0) cc_final: 0.8473 (tt0) REVERT: A 397 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 411 ASP cc_start: 0.8430 (t0) cc_final: 0.7990 (t0) REVERT: A 423 ASP cc_start: 0.8495 (m-30) cc_final: 0.8228 (m-30) REVERT: A 477 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8442 (mm-30) REVERT: A 492 GLU cc_start: 0.6753 (tp30) cc_final: 0.6474 (tm-30) REVERT: A 494 ASP cc_start: 0.8524 (m-30) cc_final: 0.8268 (m-30) REVERT: A 512 ASP cc_start: 0.8517 (t0) cc_final: 0.8279 (t0) REVERT: A 521 MET cc_start: 0.8953 (mtp) cc_final: 0.8745 (mtm) REVERT: A 525 MET cc_start: 0.9117 (mmm) cc_final: 0.8778 (mtm) REVERT: A 585 ASP cc_start: 0.8277 (t0) cc_final: 0.7827 (t0) outliers start: 8 outliers final: 2 residues processed: 81 average time/residue: 1.1236 time to fit residues: 94.9340 Evaluate side-chains 75 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.084671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.074967 restraints weight = 7883.184| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.25 r_work: 0.3016 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4643 Z= 0.175 Angle : 0.614 10.137 6326 Z= 0.312 Chirality : 0.046 0.207 714 Planarity : 0.004 0.030 797 Dihedral : 5.651 30.754 890 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.89 % Allowed : 13.87 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.10 (0.35), residues: 533 helix: 0.36 (0.64), residues: 69 sheet: 0.33 (0.41), residues: 150 loop : -0.04 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 361 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE A 486 TYR 0.017 0.001 TYR A 97 ARG 0.003 0.000 ARG A 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 6) link_NAG-ASN : angle 2.02134 ( 18) link_BETA1-4 : bond 0.00338 ( 8) link_BETA1-4 : angle 1.86777 ( 24) hydrogen bonds : bond 0.03724 ( 152) hydrogen bonds : angle 5.48279 ( 354) link_BETA1-6 : bond 0.00363 ( 1) link_BETA1-6 : angle 2.03023 ( 3) metal coordination : bond 0.00521 ( 3) SS BOND : bond 0.00628 ( 5) SS BOND : angle 1.65127 ( 10) covalent geometry : bond 0.00404 ( 4620) covalent geometry : angle 0.59118 ( 6271) *********************** 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: 9 poor density : 76 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8790 (tp30) cc_final: 0.8521 (tp30) REVERT: A 196 ASP cc_start: 0.8711 (p0) cc_final: 0.8479 (p0) REVERT: A 207 ASP cc_start: 0.8272 (t0) cc_final: 0.7879 (t0) REVERT: A 227 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8690 (p) REVERT: A 251 GLU cc_start: 0.8713 (tt0) cc_final: 0.8465 (tt0) REVERT: A 325 GLU cc_start: 0.8369 (mp0) cc_final: 0.8134 (mp0) REVERT: A 397 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7724 (mm-30) REVERT: A 411 ASP cc_start: 0.8491 (t0) cc_final: 0.8007 (t0) REVERT: A 423 ASP cc_start: 0.8503 (m-30) cc_final: 0.8232 (m-30) REVERT: A 492 GLU cc_start: 0.6741 (tp30) cc_final: 0.6389 (tm-30) REVERT: A 494 ASP cc_start: 0.8485 (m-30) cc_final: 0.8216 (m-30) REVERT: A 512 ASP cc_start: 0.8510 (t0) cc_final: 0.8287 (t0) REVERT: A 521 MET cc_start: 0.8961 (mtp) cc_final: 0.8750 (mtm) REVERT: A 525 MET cc_start: 0.9048 (mmm) cc_final: 0.8698 (mtm) REVERT: A 585 ASP cc_start: 0.8301 (t0) cc_final: 0.7802 (t0) outliers start: 9 outliers final: 4 residues processed: 82 average time/residue: 1.0777 time to fit residues: 92.2314 Evaluate side-chains 73 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 200 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.084360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.074621 restraints weight = 8049.554| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.28 r_work: 0.3007 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4643 Z= 0.172 Angle : 0.602 10.463 6326 Z= 0.308 Chirality : 0.045 0.210 714 Planarity : 0.003 0.029 797 Dihedral : 5.102 33.176 890 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.31 % Allowed : 14.92 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.05 (0.36), residues: 533 helix: 0.41 (0.64), residues: 69 sheet: 0.30 (0.42), residues: 149 loop : -0.10 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 361 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 527 TYR 0.019 0.001 TYR A 97 ARG 0.002 0.000 ARG A 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 6) link_NAG-ASN : angle 1.96971 ( 18) link_BETA1-4 : bond 0.00353 ( 8) link_BETA1-4 : angle 1.63508 ( 24) hydrogen bonds : bond 0.03672 ( 152) hydrogen bonds : angle 5.37309 ( 354) link_BETA1-6 : bond 0.00419 ( 1) link_BETA1-6 : angle 2.09455 ( 3) metal coordination : bond 0.00513 ( 3) SS BOND : bond 0.00188 ( 5) SS BOND : angle 1.32763 ( 10) covalent geometry : bond 0.00399 ( 4620) covalent geometry : angle 0.58265 ( 6271) *********************** 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 83 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8841 (tp30) cc_final: 0.8567 (tp30) REVERT: A 207 ASP cc_start: 0.8300 (t0) cc_final: 0.7895 (t0) REVERT: A 251 GLU cc_start: 0.8719 (tt0) cc_final: 0.8483 (tt0) REVERT: A 397 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7738 (mm-30) REVERT: A 411 ASP cc_start: 0.8479 (t0) cc_final: 0.7962 (t0) REVERT: A 423 ASP cc_start: 0.8512 (m-30) cc_final: 0.8232 (m-30) REVERT: A 492 GLU cc_start: 0.6836 (tp30) cc_final: 0.6557 (tm-30) REVERT: A 494 ASP cc_start: 0.8505 (m-30) cc_final: 0.8234 (m-30) REVERT: A 512 ASP cc_start: 0.8492 (t0) cc_final: 0.8263 (t0) REVERT: A 525 MET cc_start: 0.9077 (mmm) cc_final: 0.8719 (mtm) REVERT: A 585 ASP cc_start: 0.8311 (t0) cc_final: 0.7827 (t0) outliers start: 11 outliers final: 6 residues processed: 80 average time/residue: 1.0886 time to fit residues: 90.6841 Evaluate side-chains 77 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 283 THR Chi-restraints excluded: chain A residue 365 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.0170 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.085426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.075738 restraints weight = 7919.206| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.26 r_work: 0.3029 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4643 Z= 0.127 Angle : 0.595 10.775 6326 Z= 0.306 Chirality : 0.045 0.215 714 Planarity : 0.003 0.028 797 Dihedral : 4.908 33.533 890 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.68 % Allowed : 16.18 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.18 (0.36), residues: 533 helix: 0.79 (0.66), residues: 66 sheet: 0.43 (0.43), residues: 149 loop : -0.11 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 527 TYR 0.019 0.001 TYR A 97 ARG 0.003 0.000 ARG A 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 6) link_NAG-ASN : angle 1.89841 ( 18) link_BETA1-4 : bond 0.00405 ( 8) link_BETA1-4 : angle 1.50776 ( 24) hydrogen bonds : bond 0.03389 ( 152) hydrogen bonds : angle 5.28741 ( 354) link_BETA1-6 : bond 0.00530 ( 1) link_BETA1-6 : angle 1.83219 ( 3) metal coordination : bond 0.00296 ( 3) SS BOND : bond 0.00177 ( 5) SS BOND : angle 1.07683 ( 10) covalent geometry : bond 0.00289 ( 4620) covalent geometry : angle 0.57887 ( 6271) *********************** 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 82 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 207 ASP cc_start: 0.8272 (t0) cc_final: 0.7905 (t0) REVERT: A 251 GLU cc_start: 0.8733 (tt0) cc_final: 0.8497 (tt0) REVERT: A 397 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 411 ASP cc_start: 0.8470 (t0) cc_final: 0.7951 (t0) REVERT: A 423 ASP cc_start: 0.8479 (m-30) cc_final: 0.8191 (m-30) REVERT: A 492 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: A 494 ASP cc_start: 0.8474 (m-30) cc_final: 0.8197 (m-30) REVERT: A 512 ASP cc_start: 0.8481 (t0) cc_final: 0.8235 (t0) REVERT: A 525 MET cc_start: 0.9060 (mmm) cc_final: 0.8691 (mtm) REVERT: A 585 ASP cc_start: 0.8282 (t0) cc_final: 0.7775 (t0) outliers start: 8 outliers final: 4 residues processed: 78 average time/residue: 1.0707 time to fit residues: 87.1854 Evaluate side-chains 75 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 200 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 492 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 19 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.086053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.076362 restraints weight = 7946.170| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.28 r_work: 0.3044 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4643 Z= 0.110 Angle : 0.568 10.996 6326 Z= 0.292 Chirality : 0.044 0.218 714 Planarity : 0.003 0.030 797 Dihedral : 4.679 34.596 890 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.31 % Allowed : 15.55 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.21 (0.36), residues: 533 helix: 0.53 (0.64), residues: 72 sheet: 0.60 (0.44), residues: 149 loop : -0.11 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 527 TYR 0.006 0.001 TYR A 113 ARG 0.002 0.000 ARG A 578 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 6) link_NAG-ASN : angle 1.83884 ( 18) link_BETA1-4 : bond 0.00407 ( 8) link_BETA1-4 : angle 1.40208 ( 24) hydrogen bonds : bond 0.03206 ( 152) hydrogen bonds : angle 5.19825 ( 354) link_BETA1-6 : bond 0.00579 ( 1) link_BETA1-6 : angle 1.68952 ( 3) metal coordination : bond 0.00210 ( 3) SS BOND : bond 0.00212 ( 5) SS BOND : angle 0.99837 ( 10) covalent geometry : bond 0.00248 ( 4620) covalent geometry : angle 0.55296 ( 6271) *********************** 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 81 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8313 (m-30) REVERT: A 207 ASP cc_start: 0.8247 (t0) cc_final: 0.7881 (t0) REVERT: A 251 GLU cc_start: 0.8725 (tt0) cc_final: 0.8478 (tt0) REVERT: A 397 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 408 THR cc_start: 0.8776 (m) cc_final: 0.8462 (p) REVERT: A 411 ASP cc_start: 0.8480 (t0) cc_final: 0.7995 (t0) REVERT: A 423 ASP cc_start: 0.8505 (m-30) cc_final: 0.8220 (m-30) REVERT: A 492 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: A 494 ASP cc_start: 0.8429 (m-30) cc_final: 0.8199 (m-30) REVERT: A 501 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8057 (t) REVERT: A 512 ASP cc_start: 0.8469 (t0) cc_final: 0.8210 (t0) REVERT: A 525 MET cc_start: 0.9068 (mmm) cc_final: 0.8732 (mtm) outliers start: 11 outliers final: 4 residues processed: 78 average time/residue: 1.0103 time to fit residues: 82.5478 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 : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 192 ASP 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 492 GLU Chi-restraints excluded: chain A residue 501 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.0270 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.085405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.075659 restraints weight = 8009.693| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.29 r_work: 0.3033 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4643 Z= 0.140 Angle : 0.606 11.136 6326 Z= 0.310 Chirality : 0.046 0.226 714 Planarity : 0.003 0.032 797 Dihedral : 4.743 36.341 890 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.89 % Allowed : 16.81 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.31 (0.37), residues: 533 helix: 1.01 (0.66), residues: 66 sheet: 0.56 (0.45), residues: 149 loop : -0.07 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.001 PHE A 527 TYR 0.021 0.001 TYR A 97 ARG 0.002 0.000 ARG A 372 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 6) link_NAG-ASN : angle 1.86870 ( 18) link_BETA1-4 : bond 0.00382 ( 8) link_BETA1-4 : angle 1.44108 ( 24) hydrogen bonds : bond 0.03361 ( 152) hydrogen bonds : angle 5.21761 ( 354) link_BETA1-6 : bond 0.00451 ( 1) link_BETA1-6 : angle 1.87634 ( 3) metal coordination : bond 0.00364 ( 3) SS BOND : bond 0.00285 ( 5) SS BOND : angle 2.74686 ( 10) covalent geometry : bond 0.00324 ( 4620) covalent geometry : angle 0.58156 ( 6271) *********************** 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 89 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: A 207 ASP cc_start: 0.8266 (t0) cc_final: 0.7913 (t0) REVERT: A 251 GLU cc_start: 0.8731 (tt0) cc_final: 0.8482 (tt0) REVERT: A 259 CYS cc_start: 0.7677 (m) cc_final: 0.7371 (m) REVERT: A 284 ARG cc_start: 0.5076 (ttt180) cc_final: 0.2052 (ppt170) REVERT: A 397 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7587 (mm-30) REVERT: A 408 THR cc_start: 0.8796 (m) cc_final: 0.8481 (p) REVERT: A 411 ASP cc_start: 0.8490 (t0) cc_final: 0.8006 (t0) REVERT: A 423 ASP cc_start: 0.8507 (m-30) cc_final: 0.8234 (m-30) REVERT: A 492 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6462 (tm-30) REVERT: A 494 ASP cc_start: 0.8436 (m-30) cc_final: 0.8205 (m-30) REVERT: A 501 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8085 (t) REVERT: A 512 ASP cc_start: 0.8485 (t0) cc_final: 0.8224 (t0) REVERT: A 525 MET cc_start: 0.9059 (mmm) cc_final: 0.8730 (mtm) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.9997 time to fit residues: 88.9686 Evaluate side-chains 75 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 192 ASP 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 492 GLU Chi-restraints excluded: chain A residue 501 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 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 ** 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 = 0.3304 r_free = 0.3304 target = 0.084390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.074652 restraints weight = 8020.220| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.28 r_work: 0.3011 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 4643 Z= 0.225 Angle : 0.673 15.141 6326 Z= 0.342 Chirality : 0.047 0.242 714 Planarity : 0.004 0.033 797 Dihedral : 5.090 40.646 890 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.89 % Allowed : 17.65 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.14 (0.37), residues: 533 helix: 0.66 (0.65), residues: 69 sheet: 0.51 (0.45), residues: 149 loop : -0.18 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 361 HIS 0.007 0.001 HIS A 155 PHE 0.012 0.002 PHE A 486 TYR 0.012 0.002 TYR A 97 ARG 0.004 0.000 ARG A 561 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 6) link_NAG-ASN : angle 1.94020 ( 18) link_BETA1-4 : bond 0.00328 ( 8) link_BETA1-4 : angle 1.51721 ( 24) hydrogen bonds : bond 0.03674 ( 152) hydrogen bonds : angle 5.27242 ( 354) link_BETA1-6 : bond 0.00292 ( 1) link_BETA1-6 : angle 2.37652 ( 3) metal coordination : bond 0.00664 ( 3) SS BOND : bond 0.00653 ( 5) SS BOND : angle 3.06032 ( 10) covalent geometry : bond 0.00535 ( 4620) covalent geometry : angle 0.64738 ( 6271) *********************** 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 76 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8322 (m-30) REVERT: A 207 ASP cc_start: 0.8308 (t0) cc_final: 0.7933 (t0) REVERT: A 209 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8410 (tt0) REVERT: A 251 GLU cc_start: 0.8741 (tt0) cc_final: 0.8500 (tt0) REVERT: A 284 ARG cc_start: 0.4884 (ttt180) cc_final: 0.1777 (tmt170) REVERT: A 397 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7608 (mm-30) REVERT: A 408 THR cc_start: 0.8838 (m) cc_final: 0.8513 (p) REVERT: A 411 ASP cc_start: 0.8503 (t0) cc_final: 0.7970 (t0) REVERT: A 423 ASP cc_start: 0.8530 (m-30) cc_final: 0.8254 (m-30) REVERT: A 463 GLU cc_start: 0.5505 (tp30) cc_final: 0.5007 (tp30) REVERT: A 492 GLU cc_start: 0.6791 (tp30) cc_final: 0.6560 (tm-30) REVERT: A 494 ASP cc_start: 0.8489 (m-30) cc_final: 0.8245 (m-30) REVERT: A 501 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8194 (t) REVERT: A 512 ASP cc_start: 0.8504 (t0) cc_final: 0.8254 (t0) REVERT: A 525 MET cc_start: 0.9078 (mmm) cc_final: 0.8737 (mtm) outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 1.1099 time to fit residues: 84.6056 Evaluate side-chains 77 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 192 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 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 = 0.3334 r_free = 0.3334 target = 0.088088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.078587 restraints weight = 7865.454| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.24 r_work: 0.3056 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4643 Z= 0.151 Angle : 0.649 12.596 6326 Z= 0.332 Chirality : 0.046 0.218 714 Planarity : 0.003 0.030 797 Dihedral : 5.065 43.777 890 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.68 % Allowed : 17.65 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.19 (0.36), residues: 533 helix: 0.98 (0.66), residues: 66 sheet: 0.55 (0.46), residues: 148 loop : -0.20 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE A 486 TYR 0.030 0.001 TYR A 97 ARG 0.002 0.000 ARG A 561 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 6) link_NAG-ASN : angle 1.86961 ( 18) link_BETA1-4 : bond 0.00382 ( 8) link_BETA1-4 : angle 1.42906 ( 24) hydrogen bonds : bond 0.03426 ( 152) hydrogen bonds : angle 5.25845 ( 354) link_BETA1-6 : bond 0.00491 ( 1) link_BETA1-6 : angle 1.93407 ( 3) metal coordination : bond 0.00383 ( 3) SS BOND : bond 0.00423 ( 5) SS BOND : angle 2.69302 ( 10) covalent geometry : bond 0.00357 ( 4620) covalent geometry : angle 0.62765 ( 6271) ********************** 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 78 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8330 (m-30) REVERT: A 207 ASP cc_start: 0.8320 (t0) cc_final: 0.7932 (t0) REVERT: A 209 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8323 (tt0) REVERT: A 251 GLU cc_start: 0.8654 (tt0) cc_final: 0.8404 (tt0) REVERT: A 284 ARG cc_start: 0.4758 (ttt180) cc_final: 0.1764 (ppt170) REVERT: A 397 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 408 THR cc_start: 0.8819 (m) cc_final: 0.8499 (p) REVERT: A 411 ASP cc_start: 0.8508 (t0) cc_final: 0.8012 (t0) REVERT: A 423 ASP cc_start: 0.8513 (m-30) cc_final: 0.8217 (m-30) REVERT: A 463 GLU cc_start: 0.5269 (tp30) cc_final: 0.4790 (tp30) REVERT: A 492 GLU cc_start: 0.6750 (tp30) cc_final: 0.6544 (tm-30) REVERT: A 494 ASP cc_start: 0.8464 (m-30) cc_final: 0.8218 (m-30) REVERT: A 501 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8120 (t) REVERT: A 512 ASP cc_start: 0.8528 (t0) cc_final: 0.8276 (t0) REVERT: A 521 MET cc_start: 0.8994 (mtp) cc_final: 0.8764 (mtm) REVERT: A 525 MET cc_start: 0.9050 (mmm) cc_final: 0.8728 (mtm) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 1.3838 time to fit residues: 111.7516 Evaluate side-chains 80 residues out of total 477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 192 ASP 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 557 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078122 restraints weight = 7854.676| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.24 r_work: 0.3043 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4643 Z= 0.185 Angle : 0.665 13.300 6326 Z= 0.340 Chirality : 0.046 0.213 714 Planarity : 0.003 0.029 797 Dihedral : 5.119 42.490 890 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % 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 (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: 0.18 (0.36), residues: 533 helix: 0.97 (0.66), residues: 66 sheet: 0.56 (0.46), residues: 148 loop : -0.23 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 289 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE A 486 TYR 0.014 0.001 TYR A 97 ARG 0.002 0.000 ARG A 561 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 6) link_NAG-ASN : angle 1.90154 ( 18) link_BETA1-4 : bond 0.00351 ( 8) link_BETA1-4 : angle 1.46238 ( 24) hydrogen bonds : bond 0.03535 ( 152) hydrogen bonds : angle 5.27474 ( 354) link_BETA1-6 : bond 0.00431 ( 1) link_BETA1-6 : angle 2.19492 ( 3) metal coordination : bond 0.00509 ( 3) SS BOND : bond 0.00430 ( 5) SS BOND : angle 2.97706 ( 10) covalent geometry : bond 0.00440 ( 4620) covalent geometry : angle 0.64134 ( 6271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4245.69 seconds wall clock time: 75 minutes 28.44 seconds (4528.44 seconds total)