Starting phenix.real_space_refine on Sun May 11 02:30:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zya_60560/05_2025/8zya_60560.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zya_60560/05_2025/8zya_60560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zya_60560/05_2025/8zya_60560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zya_60560/05_2025/8zya_60560.map" model { file = "/net/cci-nas-00/data/ceres_data/8zya_60560/05_2025/8zya_60560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zya_60560/05_2025/8zya_60560.cif" } resolution = 2.5 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= 0.002 sd= 0.126 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4663 2.51 5 N 1211 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7306 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1464 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Chain: "D" Number of atoms: 5730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5730 Classifications: {'peptide': 698} Link IDs: {'PTRANS': 34, 'TRANS': 663} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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 Time building chain proxies: 4.54, per 1000 atoms: 0.62 Number of scatterers: 7306 At special positions: 0 Unit cell: (77.745, 102.93, 133.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1392 8.00 N 1211 7.00 C 4663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 469 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 1 " - " ASN D 53 " " NAG C 1 " - " ASN D 689 " " NAG D 901 " - " ASN D 322 " " NAG D 902 " - " ASN D 432 " " NAG E 1 " - " ASN D 546 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 993.9 milliseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1666 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 49.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.736A pdb=" N TRP A 343 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'D' and resid 24 through 53 removed outlier: 3.514A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.724A pdb=" N GLN D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 81 removed outlier: 4.544A pdb=" N ALA D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 100 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 172 through 193 Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.709A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 224 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.569A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.669A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.545A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.574A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 409 removed outlier: 3.772A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.799A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.391A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.987A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 4.032A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.635A pdb=" N GLU D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 657 removed outlier: 3.842A pdb=" N MET D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR D 641 " --> pdb=" O ASP D 637 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 642 " --> pdb=" O ASN D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 706 Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 371 Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 443 Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.928A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.218A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 618 through 621 302 hydrogen bonds defined for protein. 858 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: 1.83 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1246 1.32 - 1.45: 2165 1.45 - 1.57: 4032 1.57 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 7508 Sorted by residual: bond pdb=" N VAL D 560 " pdb=" CA VAL D 560 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.26e-02 6.30e+03 8.77e+00 bond pdb=" C GLN D 556 " pdb=" O GLN D 556 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.35e-02 5.49e+03 8.35e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" N LYS D 562 " pdb=" CA LYS D 562 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.33e-02 5.65e+03 5.65e+00 bond pdb=" N SER D 559 " pdb=" CA SER D 559 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.28e-02 6.10e+03 5.37e+00 ... (remaining 7503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 9925 2.04 - 4.09: 219 4.09 - 6.13: 33 6.13 - 8.17: 11 8.17 - 10.22: 3 Bond angle restraints: 10191 Sorted by residual: angle pdb=" N VAL A 331 " pdb=" CA VAL A 331 " pdb=" C VAL A 331 " ideal model delta sigma weight residual 113.71 106.57 7.14 9.50e-01 1.11e+00 5.65e+01 angle pdb=" C THR D 90 " pdb=" N VAL D 91 " pdb=" CA VAL D 91 " ideal model delta sigma weight residual 120.33 124.77 -4.44 8.00e-01 1.56e+00 3.08e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 115.61 108.51 7.10 1.74e+00 3.30e-01 1.66e+01 angle pdb=" N MET D 557 " pdb=" CA MET D 557 " pdb=" C MET D 557 " ideal model delta sigma weight residual 113.55 108.67 4.88 1.26e+00 6.30e-01 1.50e+01 angle pdb=" N GLN D 556 " pdb=" CA GLN D 556 " pdb=" C GLN D 556 " ideal model delta sigma weight residual 113.20 108.93 4.27 1.21e+00 6.83e-01 1.24e+01 ... (remaining 10186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4072 17.67 - 35.33: 397 35.33 - 53.00: 62 53.00 - 70.67: 11 70.67 - 88.33: 7 Dihedral angle restraints: 4549 sinusoidal: 1954 harmonic: 2595 Sorted by residual: dihedral pdb=" CA GLN D 102 " pdb=" C GLN D 102 " pdb=" N SER D 103 " pdb=" CA SER D 103 " ideal model delta harmonic sigma weight residual -180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLN D 101 " pdb=" C GLN D 101 " pdb=" N GLN D 102 " pdb=" CA GLN D 102 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ASP D 250 " pdb=" C ASP D 250 " pdb=" N THR D 251 " pdb=" CA THR D 251 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 4546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 911 0.063 - 0.125: 164 0.125 - 0.188: 10 0.188 - 0.251: 1 0.251 - 0.314: 2 Chirality restraints: 1088 Sorted by residual: chirality pdb=" C2 NAG E 2 " pdb=" C1 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" N2 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.18 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB VAL D 581 " pdb=" CA VAL D 581 " pdb=" CG1 VAL D 581 " pdb=" CG2 VAL D 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE D 678 " pdb=" CA ILE D 678 " pdb=" CG1 ILE D 678 " pdb=" CG2 ILE D 678 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1085 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 345 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO D 346 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO D 346 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 346 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " -0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO D 146 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 555 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C HIS D 555 " -0.044 2.00e-02 2.50e+03 pdb=" O HIS D 555 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN D 556 " 0.015 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2026 2.81 - 3.33: 6520 3.33 - 3.86: 12403 3.86 - 4.38: 14715 4.38 - 4.90: 25038 Nonbonded interactions: 60702 Sorted by model distance: nonbonded pdb=" O PHE D 327 " pdb=" OG SER D 331 " model vdw 2.290 3.040 nonbonded pdb=" O ASP D 499 " pdb=" OG SER D 502 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP D 382 " pdb=" OH TYR D 385 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.322 3.040 nonbonded pdb=" OH TYR A 442 " pdb=" ND1 HIS D 34 " model vdw 2.323 3.120 ... (remaining 60697 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' 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=0.00 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.330 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.004 0.063 7522 Z= 0.203 Angle : 0.745 10.571 10227 Z= 0.407 Chirality : 0.049 0.314 1088 Planarity : 0.007 0.115 1304 Dihedral : 14.034 88.333 2865 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.43 % Rotamer: Outliers : 0.13 % Allowed : 0.51 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.27), residues: 876 helix: -0.80 (0.24), residues: 409 sheet: 1.58 (0.70), residues: 42 loop : -1.37 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 566 HIS 0.007 0.001 HIS D 378 PHE 0.022 0.002 PHE A 337 TYR 0.017 0.001 TYR D 385 ARG 0.004 0.000 ARG D 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 5) link_NAG-ASN : angle 2.18395 ( 15) link_BETA1-4 : bond 0.01572 ( 3) link_BETA1-4 : angle 4.02206 ( 9) hydrogen bonds : bond 0.17116 ( 302) hydrogen bonds : angle 6.92262 ( 858) SS BOND : bond 0.00240 ( 6) SS BOND : angle 0.91467 ( 12) covalent geometry : bond 0.00403 ( 7508) covalent geometry : angle 0.73143 (10191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.838 Fit side-chains REVERT: D 49 GLU cc_start: 0.7506 (tp30) cc_final: 0.7255 (tp30) REVERT: D 60 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7514 (tm-30) REVERT: D 82 ASN cc_start: 0.7880 (m110) cc_final: 0.7605 (m-40) REVERT: D 472 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7536 (mt-10) outliers start: 1 outliers final: 2 residues processed: 108 average time/residue: 1.2913 time to fit residues: 146.9860 Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 457 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.0270 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN D 42 GLN D 58 ASN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.115742 restraints weight = 8354.445| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.51 r_work: 0.3431 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7522 Z= 0.116 Angle : 0.559 9.765 10227 Z= 0.282 Chirality : 0.041 0.253 1088 Planarity : 0.005 0.069 1304 Dihedral : 6.970 56.913 1143 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.90 % Allowed : 6.59 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 876 helix: -0.02 (0.26), residues: 420 sheet: 1.70 (0.72), residues: 42 loop : -1.25 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 427 HIS 0.006 0.001 HIS D 374 PHE 0.015 0.001 PHE D 369 TYR 0.013 0.001 TYR D 385 ARG 0.003 0.000 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 5) link_NAG-ASN : angle 1.86742 ( 15) link_BETA1-4 : bond 0.01194 ( 3) link_BETA1-4 : angle 2.82785 ( 9) hydrogen bonds : bond 0.04425 ( 302) hydrogen bonds : angle 5.01997 ( 858) SS BOND : bond 0.00369 ( 6) SS BOND : angle 0.91212 ( 12) covalent geometry : bond 0.00251 ( 7508) covalent geometry : angle 0.54856 (10191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: D 64 GLU cc_start: 0.6846 (mm-30) cc_final: 0.5953 (tm-30) REVERT: D 74 GLU cc_start: 0.6575 (pp20) cc_final: 0.6263 (pt0) REVERT: D 140 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6589 (pm20) REVERT: D 208 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: D 227 ASP cc_start: 0.6936 (p0) cc_final: 0.6691 (p0) REVERT: D 401 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7555 (t-90) REVERT: D 465 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7636 (ttp80) REVERT: D 467 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8510 (mt-10) REVERT: D 472 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7528 (mt-10) REVERT: D 564 GLN cc_start: 0.7838 (tt0) cc_final: 0.7632 (tt0) outliers start: 15 outliers final: 5 residues processed: 93 average time/residue: 1.3546 time to fit residues: 132.8467 Evaluate side-chains 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 637 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.147581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111981 restraints weight = 8376.092| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.51 r_work: 0.3386 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7522 Z= 0.140 Angle : 0.557 9.559 10227 Z= 0.280 Chirality : 0.042 0.248 1088 Planarity : 0.004 0.055 1304 Dihedral : 6.312 56.251 1140 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.15 % Allowed : 9.63 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.29), residues: 876 helix: 0.34 (0.26), residues: 419 sheet: 1.61 (0.74), residues: 42 loop : -1.19 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 349 HIS 0.005 0.001 HIS D 241 PHE 0.018 0.001 PHE D 400 TYR 0.012 0.001 TYR D 516 ARG 0.005 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 5) link_NAG-ASN : angle 2.08193 ( 15) link_BETA1-4 : bond 0.01001 ( 3) link_BETA1-4 : angle 2.68392 ( 9) hydrogen bonds : bond 0.04408 ( 302) hydrogen bonds : angle 4.70755 ( 858) SS BOND : bond 0.00368 ( 6) SS BOND : angle 0.99852 ( 12) covalent geometry : bond 0.00320 ( 7508) covalent geometry : angle 0.54573 (10191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6484 (mp) REVERT: D 49 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6052 (tm-30) REVERT: D 62 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.5885 (mtp) REVERT: D 64 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6176 (mp0) REVERT: D 74 GLU cc_start: 0.6666 (pp20) cc_final: 0.6343 (pt0) REVERT: D 140 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6786 (pm20) REVERT: D 208 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: D 367 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6365 (pp20) REVERT: D 465 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7907 (ttp80) REVERT: D 472 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7675 (mt-10) REVERT: D 564 GLN cc_start: 0.8073 (tt0) cc_final: 0.7871 (tt0) REVERT: D 640 MET cc_start: 0.7694 (tpt) cc_final: 0.7363 (mmm) outliers start: 17 outliers final: 8 residues processed: 100 average time/residue: 1.2882 time to fit residues: 136.4376 Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 637 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 0.0000 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.143609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.107884 restraints weight = 8437.847| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.50 r_work: 0.3333 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7522 Z= 0.196 Angle : 0.603 9.513 10227 Z= 0.304 Chirality : 0.045 0.256 1088 Planarity : 0.005 0.049 1304 Dihedral : 6.381 56.426 1140 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.92 % Allowed : 10.77 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.29), residues: 876 helix: 0.34 (0.27), residues: 417 sheet: 1.27 (0.74), residues: 42 loop : -1.21 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 168 HIS 0.006 0.001 HIS D 241 PHE 0.022 0.002 PHE D 400 TYR 0.015 0.002 TYR D 385 ARG 0.004 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 5) link_NAG-ASN : angle 2.34021 ( 15) link_BETA1-4 : bond 0.00939 ( 3) link_BETA1-4 : angle 2.70017 ( 9) hydrogen bonds : bond 0.04846 ( 302) hydrogen bonds : angle 4.73600 ( 858) SS BOND : bond 0.00464 ( 6) SS BOND : angle 1.11015 ( 12) covalent geometry : bond 0.00471 ( 7508) covalent geometry : angle 0.59070 (10191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6649 (mp) REVERT: D 49 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6026 (tm-30) REVERT: D 62 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.6038 (mtp) REVERT: D 64 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6025 (mp0) REVERT: D 68 LYS cc_start: 0.6590 (mttm) cc_final: 0.6389 (mttp) REVERT: D 74 GLU cc_start: 0.6686 (pp20) cc_final: 0.6351 (pt0) REVERT: D 208 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: D 401 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7813 (t-90) REVERT: D 465 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7927 (ttp80) REVERT: D 472 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7679 (mt-10) outliers start: 23 outliers final: 10 residues processed: 96 average time/residue: 1.2786 time to fit residues: 129.5145 Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 373 HIS ** 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 = 0.3834 r_free = 0.3834 target = 0.145131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.109686 restraints weight = 8374.311| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.51 r_work: 0.3296 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7522 Z= 0.133 Angle : 0.545 9.520 10227 Z= 0.273 Chirality : 0.042 0.253 1088 Planarity : 0.004 0.041 1304 Dihedral : 6.151 56.019 1140 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.66 % Allowed : 11.66 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.29), residues: 876 helix: 0.53 (0.27), residues: 412 sheet: 0.83 (0.66), residues: 52 loop : -1.15 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.014 0.001 PHE D 523 TYR 0.013 0.001 TYR D 516 ARG 0.005 0.000 ARG D 621 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 5) link_NAG-ASN : angle 2.08574 ( 15) link_BETA1-4 : bond 0.01013 ( 3) link_BETA1-4 : angle 2.62983 ( 9) hydrogen bonds : bond 0.04238 ( 302) hydrogen bonds : angle 4.61311 ( 858) SS BOND : bond 0.00339 ( 6) SS BOND : angle 0.95897 ( 12) covalent geometry : bond 0.00309 ( 7508) covalent geometry : angle 0.53297 (10191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6569 (mp) REVERT: D 49 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.5932 (tm-30) REVERT: D 62 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6016 (mtp) REVERT: D 64 GLU cc_start: 0.6841 (mm-30) cc_final: 0.5996 (mp0) REVERT: D 74 GLU cc_start: 0.6579 (pp20) cc_final: 0.6237 (pt0) REVERT: D 140 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7062 (pm20) REVERT: D 208 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: D 401 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7837 (t-90) REVERT: D 472 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7628 (mt-10) REVERT: D 564 GLN cc_start: 0.8287 (tt0) cc_final: 0.8037 (tt0) REVERT: D 674 LEU cc_start: 0.7670 (tp) cc_final: 0.7442 (tt) outliers start: 21 outliers final: 10 residues processed: 93 average time/residue: 1.2478 time to fit residues: 122.6655 Evaluate side-chains 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 62 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 373 HIS ** 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 = 0.3839 r_free = 0.3839 target = 0.145637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110145 restraints weight = 8371.994| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.51 r_work: 0.3299 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7522 Z= 0.128 Angle : 0.542 9.525 10227 Z= 0.270 Chirality : 0.042 0.250 1088 Planarity : 0.004 0.041 1304 Dihedral : 6.041 55.994 1140 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.66 % Allowed : 12.42 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.29), residues: 876 helix: 0.63 (0.27), residues: 413 sheet: 0.79 (0.65), residues: 52 loop : -1.12 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.015 0.001 PHE D 523 TYR 0.012 0.001 TYR D 516 ARG 0.006 0.000 ARG D 621 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 5) link_NAG-ASN : angle 2.07534 ( 15) link_BETA1-4 : bond 0.01025 ( 3) link_BETA1-4 : angle 2.60230 ( 9) hydrogen bonds : bond 0.04126 ( 302) hydrogen bonds : angle 4.54649 ( 858) SS BOND : bond 0.00343 ( 6) SS BOND : angle 0.91627 ( 12) covalent geometry : bond 0.00295 ( 7508) covalent geometry : angle 0.53061 (10191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6544 (mp) REVERT: D 49 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.5931 (tm-30) REVERT: D 62 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6309 (mpp) REVERT: D 64 GLU cc_start: 0.6668 (mm-30) cc_final: 0.5939 (mp0) REVERT: D 74 GLU cc_start: 0.6639 (pp20) cc_final: 0.6296 (pt0) REVERT: D 208 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: D 472 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7646 (mt-10) REVERT: D 564 GLN cc_start: 0.8275 (tt0) cc_final: 0.8005 (tt0) REVERT: D 674 LEU cc_start: 0.7686 (tp) cc_final: 0.7449 (tt) outliers start: 21 outliers final: 11 residues processed: 94 average time/residue: 1.1949 time to fit residues: 119.1450 Evaluate side-chains 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 373 HIS ** 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 = 0.3839 r_free = 0.3839 target = 0.145554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110163 restraints weight = 8443.373| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.51 r_work: 0.3293 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7522 Z= 0.133 Angle : 0.550 9.528 10227 Z= 0.274 Chirality : 0.042 0.251 1088 Planarity : 0.004 0.040 1304 Dihedral : 6.028 55.954 1140 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.66 % Allowed : 12.93 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.29), residues: 876 helix: 0.61 (0.27), residues: 413 sheet: 0.80 (0.66), residues: 52 loop : -1.10 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.015 0.001 PHE D 523 TYR 0.012 0.001 TYR D 516 ARG 0.006 0.000 ARG D 621 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 5) link_NAG-ASN : angle 2.08354 ( 15) link_BETA1-4 : bond 0.01002 ( 3) link_BETA1-4 : angle 2.58419 ( 9) hydrogen bonds : bond 0.04120 ( 302) hydrogen bonds : angle 4.54002 ( 858) SS BOND : bond 0.00346 ( 6) SS BOND : angle 0.91323 ( 12) covalent geometry : bond 0.00310 ( 7508) covalent geometry : angle 0.53915 (10191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6541 (mp) REVERT: D 49 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.5932 (tm-30) REVERT: D 62 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6326 (mpp) REVERT: D 64 GLU cc_start: 0.6649 (mm-30) cc_final: 0.5456 (tm-30) REVERT: D 74 GLU cc_start: 0.6636 (pp20) cc_final: 0.6286 (pt0) REVERT: D 208 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: D 465 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7516 (ttp80) REVERT: D 467 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8425 (mt-10) REVERT: D 472 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7633 (mt-10) REVERT: D 564 GLN cc_start: 0.8247 (tt0) cc_final: 0.8010 (tt0) REVERT: D 674 LEU cc_start: 0.7694 (tp) cc_final: 0.7446 (tt) outliers start: 21 outliers final: 14 residues processed: 95 average time/residue: 1.2241 time to fit residues: 122.8876 Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 637 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 15 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN ** D 373 HIS ** 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 = 0.3854 r_free = 0.3854 target = 0.147083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111670 restraints weight = 8411.364| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.52 r_work: 0.3319 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7522 Z= 0.109 Angle : 0.531 9.529 10227 Z= 0.264 Chirality : 0.041 0.248 1088 Planarity : 0.004 0.039 1304 Dihedral : 5.898 55.836 1140 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.79 % Allowed : 12.93 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.29), residues: 876 helix: 0.70 (0.27), residues: 413 sheet: 0.82 (0.66), residues: 52 loop : -1.06 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.013 0.001 PHE D 523 TYR 0.012 0.001 TYR D 516 ARG 0.007 0.000 ARG D 621 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 5) link_NAG-ASN : angle 1.93912 ( 15) link_BETA1-4 : bond 0.01045 ( 3) link_BETA1-4 : angle 2.53776 ( 9) hydrogen bonds : bond 0.03855 ( 302) hydrogen bonds : angle 4.45702 ( 858) SS BOND : bond 0.00285 ( 6) SS BOND : angle 0.84428 ( 12) covalent geometry : bond 0.00244 ( 7508) covalent geometry : angle 0.52060 (10191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6589 (mp) REVERT: D 49 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.5922 (tm-30) REVERT: D 62 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6385 (mpp) REVERT: D 64 GLU cc_start: 0.6762 (mm-30) cc_final: 0.5778 (tm-30) REVERT: D 74 GLU cc_start: 0.6643 (pp20) cc_final: 0.6279 (pt0) REVERT: D 208 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: D 465 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7617 (ttp80) REVERT: D 467 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8418 (mt-10) REVERT: D 472 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7682 (mt-10) REVERT: D 564 GLN cc_start: 0.8124 (tt0) cc_final: 0.7878 (tt0) REVERT: D 640 MET cc_start: 0.7637 (tpt) cc_final: 0.7316 (mmm) REVERT: D 674 LEU cc_start: 0.7694 (tp) cc_final: 0.7456 (tt) outliers start: 22 outliers final: 12 residues processed: 96 average time/residue: 1.3194 time to fit residues: 134.3138 Evaluate side-chains 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 76 optimal weight: 0.0370 chunk 18 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 373 HIS ** 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 = 0.3837 r_free = 0.3837 target = 0.145475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110024 restraints weight = 8407.318| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.51 r_work: 0.3280 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7522 Z= 0.145 Angle : 0.557 9.536 10227 Z= 0.277 Chirality : 0.042 0.251 1088 Planarity : 0.004 0.040 1304 Dihedral : 5.992 56.013 1140 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.28 % Allowed : 14.20 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.29), residues: 876 helix: 0.69 (0.27), residues: 413 sheet: 0.82 (0.66), residues: 52 loop : -1.08 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.005 0.001 HIS D 241 PHE 0.016 0.001 PHE D 523 TYR 0.012 0.001 TYR D 183 ARG 0.009 0.001 ARG D 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 5) link_NAG-ASN : angle 2.12480 ( 15) link_BETA1-4 : bond 0.00989 ( 3) link_BETA1-4 : angle 2.56347 ( 9) hydrogen bonds : bond 0.04186 ( 302) hydrogen bonds : angle 4.51532 ( 858) SS BOND : bond 0.00369 ( 6) SS BOND : angle 0.93716 ( 12) covalent geometry : bond 0.00342 ( 7508) covalent geometry : angle 0.54534 (10191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6662 (mp) REVERT: D 49 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6001 (tm-30) REVERT: D 64 GLU cc_start: 0.6766 (mm-30) cc_final: 0.5701 (tm-30) REVERT: D 74 GLU cc_start: 0.6671 (pp20) cc_final: 0.6306 (pt0) REVERT: D 208 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: D 467 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8455 (mt-10) REVERT: D 472 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7743 (mt-10) REVERT: D 674 LEU cc_start: 0.7725 (tp) cc_final: 0.7494 (tt) outliers start: 18 outliers final: 12 residues processed: 93 average time/residue: 1.2516 time to fit residues: 123.0901 Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 48 optimal weight: 0.0970 chunk 15 optimal weight: 0.0770 chunk 80 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 373 HIS ** 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 = 0.3854 r_free = 0.3854 target = 0.147142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111691 restraints weight = 8494.948| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.53 r_work: 0.3320 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7522 Z= 0.113 Angle : 0.538 9.531 10227 Z= 0.268 Chirality : 0.041 0.247 1088 Planarity : 0.004 0.039 1304 Dihedral : 5.893 55.770 1140 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.41 % Allowed : 14.45 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.29), residues: 876 helix: 0.76 (0.27), residues: 413 sheet: 0.84 (0.66), residues: 52 loop : -1.04 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.013 0.001 PHE D 523 TYR 0.013 0.001 TYR D 50 ARG 0.008 0.000 ARG D 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 5) link_NAG-ASN : angle 1.96391 ( 15) link_BETA1-4 : bond 0.01028 ( 3) link_BETA1-4 : angle 2.51842 ( 9) hydrogen bonds : bond 0.03889 ( 302) hydrogen bonds : angle 4.45261 ( 858) SS BOND : bond 0.00298 ( 6) SS BOND : angle 0.85834 ( 12) covalent geometry : bond 0.00256 ( 7508) covalent geometry : angle 0.52806 (10191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6624 (mp) REVERT: D 49 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5944 (tm-30) REVERT: D 64 GLU cc_start: 0.6735 (mm-30) cc_final: 0.5691 (tm-30) REVERT: D 74 GLU cc_start: 0.6657 (pp20) cc_final: 0.6289 (pt0) REVERT: D 208 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: D 299 ASN cc_start: 0.7521 (m-40) cc_final: 0.7035 (t0) REVERT: D 325 GLU cc_start: 0.7170 (tp30) cc_final: 0.6748 (tm-30) REVERT: D 365 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.7133 (p) REVERT: D 465 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7562 (ttp80) REVERT: D 467 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8409 (mt-10) REVERT: D 472 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7701 (mt-10) REVERT: D 674 LEU cc_start: 0.7706 (tp) cc_final: 0.7491 (tt) REVERT: D 707 ARG cc_start: 0.6434 (tpt-90) cc_final: 0.6067 (tpt-90) REVERT: D 708 SER cc_start: 0.7223 (m) cc_final: 0.6953 (p) outliers start: 19 outliers final: 12 residues processed: 95 average time/residue: 1.2175 time to fit residues: 122.3616 Evaluate side-chains 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 27 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 34 optimal weight: 0.0980 chunk 63 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 373 HIS ** 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 = 0.3873 r_free = 0.3873 target = 0.148766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113451 restraints weight = 8315.117| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.51 r_work: 0.3333 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7522 Z= 0.101 Angle : 0.523 9.545 10227 Z= 0.259 Chirality : 0.040 0.244 1088 Planarity : 0.004 0.039 1304 Dihedral : 5.752 55.770 1140 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.03 % Allowed : 14.70 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.29), residues: 876 helix: 0.83 (0.27), residues: 415 sheet: 0.87 (0.67), residues: 52 loop : -1.03 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.012 0.001 PHE D 523 TYR 0.013 0.001 TYR D 50 ARG 0.008 0.001 ARG D 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 5) link_NAG-ASN : angle 1.85987 ( 15) link_BETA1-4 : bond 0.01044 ( 3) link_BETA1-4 : angle 2.48074 ( 9) hydrogen bonds : bond 0.03661 ( 302) hydrogen bonds : angle 4.37225 ( 858) SS BOND : bond 0.00262 ( 6) SS BOND : angle 0.81744 ( 12) covalent geometry : bond 0.00224 ( 7508) covalent geometry : angle 0.51341 (10191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6177.98 seconds wall clock time: 107 minutes 13.36 seconds (6433.36 seconds total)