Starting phenix.real_space_refine on Thu Jul 2 04:20:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fdg_31542/07_2026/7fdg_31542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdg_31542/07_2026/7fdg_31542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7fdg_31542/07_2026/7fdg_31542.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fdg_31542/07_2026/7fdg_31542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fdg_31542/07_2026/7fdg_31542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdg_31542/07_2026/7fdg_31542.map" model { file = "/net/cci-nas-00/data/ceres_data/7fdg_31542/07_2026/7fdg_31542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdg_31542/07_2026/7fdg_31542.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.724 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 35 5.16 5 C 4134 2.51 5 N 1063 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6459 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4847 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4840 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 597, 4840 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 4968 Chain: "E" Number of atoms: 1542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1573 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.64, per 1000 atoms: 0.41 Number of scatterers: 6459 At special positions: 0 Unit cell: (116.48, 87.36, 80.08, 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 35 16.00 O 1227 8.00 N 1063 7.00 C 4134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.02 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 546 " " NAG A 704 " - " ASN A 90 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 624.1 milliseconds 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 56.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.896A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.641A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 4.149A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.689A pdb=" N TYR A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.786A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.031A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.616A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 448 through 465 removed outlier: 3.993A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.700A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.332A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.601A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.672A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.216A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.004A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.903A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.709A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.659A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.850A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.652A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 322 hydrogen bonds defined for protein. 916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2068 1.35 - 1.47: 1800 1.47 - 1.60: 2721 1.60 - 1.72: 0 1.72 - 1.85: 54 Bond restraints: 6643 Sorted by residual: bond pdb=" C GLY A 319 " pdb=" N LEU A 320 " ideal model delta sigma weight residual 1.329 1.279 0.050 1.86e-02 2.89e+03 7.16e+00 bond pdb=" C VAL A 283 " pdb=" N PRO A 284 " ideal model delta sigma weight residual 1.336 1.308 0.028 1.23e-02 6.61e+03 5.19e+00 bond pdb=" C TYR E 495 " pdb=" N GLY E 496 " ideal model delta sigma weight residual 1.332 1.323 0.009 5.00e-03 4.00e+04 3.39e+00 bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.66e+00 bond pdb=" CA CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sigma weight residual 1.530 1.508 0.022 1.53e-02 4.27e+03 2.13e+00 ... (remaining 6638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 8632 1.82 - 3.65: 351 3.65 - 5.47: 41 5.47 - 7.29: 10 7.29 - 9.12: 4 Bond angle restraints: 9038 Sorted by residual: angle pdb=" C PHE E 464 " pdb=" N GLU E 465 " pdb=" CA GLU E 465 " ideal model delta sigma weight residual 122.93 115.46 7.47 1.45e+00 4.76e-01 2.66e+01 angle pdb=" CA CYS E 379 " pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " ideal model delta sigma weight residual 114.40 123.52 -9.12 2.30e+00 1.89e-01 1.57e+01 angle pdb=" N CYS E 379 " pdb=" CA CYS E 379 " pdb=" C CYS E 379 " ideal model delta sigma weight residual 107.88 113.28 -5.40 1.41e+00 5.03e-01 1.47e+01 angle pdb=" CA PHE E 464 " pdb=" C PHE E 464 " pdb=" N GLU E 465 " ideal model delta sigma weight residual 116.21 120.46 -4.25 1.29e+00 6.01e-01 1.09e+01 angle pdb=" C GLN E 409 " pdb=" N ILE E 410 " pdb=" CA ILE E 410 " ideal model delta sigma weight residual 122.59 118.97 3.62 1.10e+00 8.26e-01 1.08e+01 ... (remaining 9033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3414 17.31 - 34.63: 350 34.63 - 51.94: 72 51.94 - 69.26: 24 69.26 - 86.57: 13 Dihedral angle restraints: 3873 sinusoidal: 1544 harmonic: 2329 Sorted by residual: dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 10.31 82.69 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CA VAL E 524 " pdb=" C VAL E 524 " pdb=" N CYS E 525 " pdb=" CA CYS E 525 " ideal model delta harmonic sigma weight residual 180.00 143.31 36.69 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 30.17 62.83 1 1.00e+01 1.00e-02 5.22e+01 ... (remaining 3870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 542 0.035 - 0.071: 290 0.071 - 0.106: 107 0.106 - 0.142: 20 0.142 - 0.177: 3 Chirality restraints: 962 Sorted by residual: chirality pdb=" CA CYS E 379 " pdb=" N CYS E 379 " pdb=" C CYS E 379 " pdb=" CB CYS E 379 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CB ILE E 410 " pdb=" CA ILE E 410 " pdb=" CG1 ILE E 410 " pdb=" CG2 ILE E 410 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 959 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A 500 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 283 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 284 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 473 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C TRP A 473 " -0.030 2.00e-02 2.50e+03 pdb=" O TRP A 473 " 0.011 2.00e-02 2.50e+03 pdb=" N MET A 474 " 0.010 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 170 2.63 - 3.20: 6699 3.20 - 3.76: 10796 3.76 - 4.33: 14302 4.33 - 4.90: 21797 Nonbonded interactions: 53764 Sorted by model distance: nonbonded pdb=" O THR A 118 " pdb=" OG1 THR A 122 " model vdw 2.061 3.040 nonbonded pdb=" O ASN A 103 " pdb=" OG SER A 106 " model vdw 2.093 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR E 500 " model vdw 2.138 3.040 nonbonded pdb=" O HIS A 417 " pdb=" OG SER A 420 " model vdw 2.142 3.040 nonbonded pdb=" O THR A 449 " pdb=" OG1 THR A 453 " model vdw 2.157 3.040 ... (remaining 53759 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.220 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 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:1.430 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 0.007 0.050 6655 Z= 0.329 Angle : 0.870 9.117 9067 Z= 0.493 Chirality : 0.047 0.177 962 Planarity : 0.005 0.044 1166 Dihedral : 15.844 86.573 2360 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.29 % Allowed : 6.55 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.25), residues: 789 helix: -1.83 (0.22), residues: 385 sheet: -1.82 (0.66), residues: 52 loop : -2.73 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 169 TYR 0.029 0.002 TYR E 380 PHE 0.020 0.002 PHE A 400 TRP 0.020 0.002 TRP A 165 HIS 0.006 0.002 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.33 ( 6643) covalent geometry : angle 0.84766 / 0.49 ( 9038) SS BOND : bond 0.00709 / 0.38 ( 7) SS BOND : angle 3.08745 / 1.77 ( 14) hydrogen bonds : bond 0.14417 / 8.93 ( 322) hydrogen bonds : angle 6.69268 / 4.76 ( 916) link_NAG-ASN : bond 0.00527 / 0.32 ( 5) link_NAG-ASN : angle 3.92781 / 2.30 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9485 (mt) cc_final: 0.9246 (mt) REVERT: A 76 GLN cc_start: 0.9323 (mm-40) cc_final: 0.8964 (mm-40) REVERT: A 97 LEU cc_start: 0.9367 (mt) cc_final: 0.9134 (mt) REVERT: A 127 TYR cc_start: 0.6916 (t80) cc_final: 0.6595 (t80) REVERT: A 224 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7901 (mt-10) REVERT: A 249 MET cc_start: 0.7900 (ttp) cc_final: 0.7629 (ttp) REVERT: A 258 PRO cc_start: 0.7916 (Cg_endo) cc_final: 0.7383 (Cg_exo) REVERT: A 362 THR cc_start: 0.8996 (m) cc_final: 0.8776 (m) REVERT: A 406 GLU cc_start: 0.8591 (tt0) cc_final: 0.8372 (tt0) REVERT: A 452 PHE cc_start: 0.9062 (t80) cc_final: 0.8799 (t80) REVERT: A 455 MET cc_start: 0.9132 (tmm) cc_final: 0.8472 (tmm) REVERT: A 481 LYS cc_start: 0.9130 (tppp) cc_final: 0.8662 (ttpt) REVERT: A 482 ARG cc_start: 0.8985 (mtm-85) cc_final: 0.8438 (mtt180) REVERT: A 485 VAL cc_start: 0.8270 (t) cc_final: 0.7973 (t) REVERT: A 499 ASP cc_start: 0.8617 (m-30) cc_final: 0.8154 (t70) REVERT: A 503 LEU cc_start: 0.8573 (tp) cc_final: 0.8357 (tp) REVERT: E 357 ARG cc_start: 0.8576 (ttt180) cc_final: 0.7204 (mtt180) REVERT: E 418 ILE cc_start: 0.9382 (mp) cc_final: 0.9077 (mp) REVERT: E 455 LEU cc_start: 0.9386 (tp) cc_final: 0.9149 (tp) REVERT: E 481 ASN cc_start: 0.8277 (t0) cc_final: 0.7975 (t0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.0767 time to fit residues: 19.6236 Evaluate side-chains 136 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 277 ASN A 338 ASN A 417 HIS A 535 HIS A 552 GLN A 556 ASN E 388 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.112261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.093010 restraints weight = 50883.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.097796 restraints weight = 16933.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.100907 restraints weight = 8623.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.103004 restraints weight = 5237.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.104449 restraints weight = 3542.879| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6655 Z= 0.203 Angle : 0.778 8.803 9067 Z= 0.396 Chirality : 0.048 0.225 962 Planarity : 0.006 0.052 1166 Dihedral : 5.729 30.214 863 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.89 % Allowed : 15.87 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.28), residues: 789 helix: -0.23 (0.25), residues: 378 sheet: -1.67 (0.68), residues: 51 loop : -1.77 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 219 TYR 0.029 0.002 TYR A 183 PHE 0.020 0.002 PHE A 588 TRP 0.020 0.002 TRP A 477 HIS 0.006 0.002 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 ( 6643) covalent geometry : angle 0.75555 / 0.39 ( 9038) SS BOND : bond 0.00782 / 0.45 ( 7) SS BOND : angle 2.81974 / 1.66 ( 14) hydrogen bonds : bond 0.05219 / 3.42 ( 322) hydrogen bonds : angle 5.52269 / 3.94 ( 916) link_NAG-ASN : bond 0.00363 / 0.22 ( 5) link_NAG-ASN : angle 3.75976 / 2.12 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9577 (mt) cc_final: 0.9336 (mt) REVERT: A 76 GLN cc_start: 0.9377 (mm-40) cc_final: 0.8583 (mm-40) REVERT: A 127 TYR cc_start: 0.7045 (t80) cc_final: 0.6806 (t80) REVERT: A 249 MET cc_start: 0.7949 (ttp) cc_final: 0.7671 (ttp) REVERT: A 258 PRO cc_start: 0.7819 (Cg_endo) cc_final: 0.7265 (Cg_exo) REVERT: A 275 TRP cc_start: 0.8819 (m-10) cc_final: 0.8590 (m-10) REVERT: A 323 MET cc_start: 0.8256 (mmm) cc_final: 0.7371 (mmm) REVERT: A 332 MET cc_start: 0.8147 (tpt) cc_final: 0.7908 (tmm) REVERT: A 340 GLN cc_start: 0.7163 (pt0) cc_final: 0.6953 (tp-100) REVERT: A 353 LYS cc_start: 0.9060 (tttt) cc_final: 0.7948 (ttmt) REVERT: A 360 MET cc_start: 0.8018 (tmm) cc_final: 0.7714 (tpt) REVERT: A 392 LEU cc_start: 0.9304 (mm) cc_final: 0.9033 (mm) REVERT: A 398 GLU cc_start: 0.8341 (pt0) cc_final: 0.8092 (pt0) REVERT: A 455 MET cc_start: 0.9186 (tmm) cc_final: 0.8906 (tmm) REVERT: A 481 LYS cc_start: 0.8958 (tppp) cc_final: 0.8528 (ttpt) REVERT: A 483 GLU cc_start: 0.9219 (tp30) cc_final: 0.8684 (mm-30) REVERT: A 485 VAL cc_start: 0.8543 (t) cc_final: 0.8315 (t) REVERT: A 499 ASP cc_start: 0.8349 (m-30) cc_final: 0.7963 (t70) REVERT: A 503 LEU cc_start: 0.8794 (tp) cc_final: 0.8579 (tp) REVERT: E 357 ARG cc_start: 0.8626 (ttt180) cc_final: 0.7241 (mtt180) REVERT: E 424 LYS cc_start: 0.9004 (tppt) cc_final: 0.8796 (tppt) REVERT: E 444 LYS cc_start: 0.7801 (ptmm) cc_final: 0.6190 (mttt) outliers start: 11 outliers final: 7 residues processed: 172 average time/residue: 0.0706 time to fit residues: 16.5894 Evaluate side-chains 151 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 588 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS E 409 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.116338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098002 restraints weight = 27863.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.102170 restraints weight = 12512.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104930 restraints weight = 7171.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106723 restraints weight = 4690.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.108015 restraints weight = 3394.308| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6655 Z= 0.155 Angle : 0.732 9.259 9067 Z= 0.368 Chirality : 0.045 0.156 962 Planarity : 0.005 0.055 1166 Dihedral : 5.359 26.594 863 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.04 % Allowed : 16.74 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.29), residues: 789 helix: 0.41 (0.25), residues: 379 sheet: -1.64 (0.64), residues: 62 loop : -1.45 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.025 0.002 TYR A 183 PHE 0.027 0.002 PHE A 230 TRP 0.019 0.001 TRP A 477 HIS 0.007 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 6643) covalent geometry : angle 0.71458 / 0.36 ( 9038) SS BOND : bond 0.00597 / 0.37 ( 7) SS BOND : angle 2.46922 / 1.46 ( 14) hydrogen bonds : bond 0.04716 / 3.15 ( 322) hydrogen bonds : angle 5.15037 / 3.65 ( 916) link_NAG-ASN : bond 0.00288 / 0.17 ( 5) link_NAG-ASN : angle 3.27935 / 1.89 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8765 (t80) cc_final: 0.8540 (t80) REVERT: A 76 GLN cc_start: 0.9305 (mm-40) cc_final: 0.8744 (mm-40) REVERT: A 82 MET cc_start: 0.9252 (mtm) cc_final: 0.9005 (mtm) REVERT: A 127 TYR cc_start: 0.7081 (t80) cc_final: 0.6815 (t80) REVERT: A 249 MET cc_start: 0.7854 (ttp) cc_final: 0.7636 (ttp) REVERT: A 258 PRO cc_start: 0.7867 (Cg_endo) cc_final: 0.7418 (Cg_exo) REVERT: A 275 TRP cc_start: 0.8759 (m-10) cc_final: 0.8451 (m-10) REVERT: A 323 MET cc_start: 0.8025 (mmm) cc_final: 0.6777 (mmm) REVERT: A 332 MET cc_start: 0.8195 (tpt) cc_final: 0.7925 (tpt) REVERT: A 340 GLN cc_start: 0.7111 (pt0) cc_final: 0.6842 (tp-100) REVERT: A 353 LYS cc_start: 0.8952 (tttt) cc_final: 0.7793 (ttmt) REVERT: A 360 MET cc_start: 0.7982 (mmm) cc_final: 0.7245 (tpt) REVERT: A 376 MET cc_start: 0.9172 (mmm) cc_final: 0.8859 (tpt) REVERT: A 398 GLU cc_start: 0.8347 (pt0) cc_final: 0.8032 (pt0) REVERT: A 406 GLU cc_start: 0.8854 (tt0) cc_final: 0.8433 (tt0) REVERT: A 452 PHE cc_start: 0.8605 (t80) cc_final: 0.8405 (t80) REVERT: A 455 MET cc_start: 0.9048 (tmm) cc_final: 0.8798 (tmm) REVERT: A 481 LYS cc_start: 0.8875 (tppp) cc_final: 0.8464 (ttpt) REVERT: A 483 GLU cc_start: 0.9214 (tp30) cc_final: 0.8679 (mm-30) REVERT: A 485 VAL cc_start: 0.8674 (t) cc_final: 0.8455 (t) REVERT: A 499 ASP cc_start: 0.8071 (m-30) cc_final: 0.7806 (t0) REVERT: A 503 LEU cc_start: 0.8866 (tp) cc_final: 0.8656 (tp) REVERT: A 567 THR cc_start: 0.9168 (m) cc_final: 0.8891 (p) REVERT: E 357 ARG cc_start: 0.8530 (ttt180) cc_final: 0.7206 (mtt180) REVERT: E 421 TYR cc_start: 0.8667 (m-10) cc_final: 0.8450 (m-10) REVERT: E 444 LYS cc_start: 0.7788 (ptmm) cc_final: 0.6351 (mttt) REVERT: E 455 LEU cc_start: 0.9234 (tp) cc_final: 0.9018 (tp) REVERT: E 509 ARG cc_start: 0.8383 (mtt180) cc_final: 0.7905 (mmm-85) outliers start: 12 outliers final: 7 residues processed: 176 average time/residue: 0.0654 time to fit residues: 15.7240 Evaluate side-chains 166 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS A A 380 GLN E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.113731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094823 restraints weight = 36569.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.099299 restraints weight = 15021.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.102220 restraints weight = 8304.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.104256 restraints weight = 5306.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105610 restraints weight = 3724.397| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6655 Z= 0.178 Angle : 0.723 7.390 9067 Z= 0.366 Chirality : 0.045 0.187 962 Planarity : 0.005 0.047 1166 Dihedral : 5.340 25.467 863 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.77 % Allowed : 18.34 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.29), residues: 789 helix: 0.57 (0.25), residues: 384 sheet: -1.39 (0.67), residues: 60 loop : -1.36 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 393 TYR 0.029 0.002 TYR A 381 PHE 0.032 0.002 PHE A 274 TRP 0.033 0.002 TRP A 477 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 6643) covalent geometry : angle 0.70717 / 0.36 ( 9038) SS BOND : bond 0.00485 / 0.30 ( 7) SS BOND : angle 2.36368 / 1.40 ( 14) hydrogen bonds : bond 0.04577 / 3.03 ( 322) hydrogen bonds : angle 5.05115 / 3.59 ( 916) link_NAG-ASN : bond 0.00359 / 0.21 ( 5) link_NAG-ASN : angle 3.03811 / 1.76 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8835 (t80) cc_final: 0.8434 (t80) REVERT: A 127 TYR cc_start: 0.7100 (t80) cc_final: 0.6825 (t80) REVERT: A 249 MET cc_start: 0.7837 (ttp) cc_final: 0.7602 (ttp) REVERT: A 258 PRO cc_start: 0.7837 (Cg_endo) cc_final: 0.7402 (Cg_exo) REVERT: A 323 MET cc_start: 0.7963 (mmm) cc_final: 0.6989 (mmm) REVERT: A 353 LYS cc_start: 0.8995 (tttt) cc_final: 0.7927 (ttmt) REVERT: A 376 MET cc_start: 0.9181 (mmm) cc_final: 0.8844 (tpt) REVERT: A 383 MET cc_start: 0.8881 (tpt) cc_final: 0.8656 (tpt) REVERT: A 392 LEU cc_start: 0.9438 (mm) cc_final: 0.8896 (mm) REVERT: A 398 GLU cc_start: 0.8382 (pt0) cc_final: 0.8144 (pt0) REVERT: A 406 GLU cc_start: 0.8895 (tt0) cc_final: 0.8192 (tt0) REVERT: A 481 LYS cc_start: 0.8917 (tppp) cc_final: 0.8524 (ttpt) REVERT: A 483 GLU cc_start: 0.9210 (tp30) cc_final: 0.8680 (mm-30) REVERT: A 487 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8105 (m) REVERT: A 499 ASP cc_start: 0.8295 (m-30) cc_final: 0.7766 (t70) REVERT: A 567 THR cc_start: 0.9162 (m) cc_final: 0.8887 (p) REVERT: E 357 ARG cc_start: 0.8491 (ttt180) cc_final: 0.7300 (mtt180) REVERT: E 396 TYR cc_start: 0.8650 (m-80) cc_final: 0.8147 (m-10) REVERT: E 409 GLN cc_start: 0.9473 (mm110) cc_final: 0.8981 (mp10) REVERT: E 421 TYR cc_start: 0.8616 (m-10) cc_final: 0.8250 (m-10) REVERT: E 423 TYR cc_start: 0.8677 (t80) cc_final: 0.7574 (t80) REVERT: E 442 ASP cc_start: 0.8972 (m-30) cc_final: 0.8046 (m-30) REVERT: E 444 LYS cc_start: 0.7940 (ptmm) cc_final: 0.6518 (mttt) REVERT: E 455 LEU cc_start: 0.9246 (tp) cc_final: 0.9026 (tp) REVERT: E 509 ARG cc_start: 0.8412 (mtt180) cc_final: 0.7797 (mmm-85) outliers start: 18 outliers final: 12 residues processed: 176 average time/residue: 0.0702 time to fit residues: 16.7421 Evaluate side-chains 176 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.117344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.098978 restraints weight = 33829.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.103306 restraints weight = 14430.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.106170 restraints weight = 8046.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108085 restraints weight = 5145.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.109338 restraints weight = 3624.791| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6655 Z= 0.149 Angle : 0.731 11.624 9067 Z= 0.364 Chirality : 0.044 0.141 962 Planarity : 0.005 0.050 1166 Dihedral : 5.084 23.826 863 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.04 % Allowed : 20.09 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.30), residues: 789 helix: 0.75 (0.26), residues: 384 sheet: -1.10 (0.71), residues: 58 loop : -1.25 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.030 0.002 TYR A 381 PHE 0.028 0.002 PHE A 230 TRP 0.042 0.002 TRP A 477 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 6643) covalent geometry : angle 0.71882 / 0.36 ( 9038) SS BOND : bond 0.00517 / 0.34 ( 7) SS BOND : angle 2.17257 / 1.28 ( 14) hydrogen bonds : bond 0.04353 / 2.88 ( 322) hydrogen bonds : angle 4.92703 / 3.49 ( 916) link_NAG-ASN : bond 0.00255 / 0.15 ( 5) link_NAG-ASN : angle 2.69277 / 1.60 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8758 (t80) cc_final: 0.8433 (t80) REVERT: A 82 MET cc_start: 0.8938 (mtm) cc_final: 0.8700 (mtm) REVERT: A 123 MET cc_start: 0.6794 (mmm) cc_final: 0.6353 (mmm) REVERT: A 258 PRO cc_start: 0.7834 (Cg_endo) cc_final: 0.7407 (Cg_exo) REVERT: A 297 MET cc_start: 0.8432 (tpp) cc_final: 0.8041 (tpp) REVERT: A 323 MET cc_start: 0.7866 (mmm) cc_final: 0.7103 (mmm) REVERT: A 349 TRP cc_start: 0.7899 (m-10) cc_final: 0.7481 (m-10) REVERT: A 353 LYS cc_start: 0.8861 (mttt) cc_final: 0.7754 (ttmt) REVERT: A 376 MET cc_start: 0.9097 (mmm) cc_final: 0.8793 (tpt) REVERT: A 392 LEU cc_start: 0.9212 (mm) cc_final: 0.9004 (mm) REVERT: A 398 GLU cc_start: 0.8283 (pt0) cc_final: 0.8024 (pt0) REVERT: A 430 GLU cc_start: 0.7527 (tp30) cc_final: 0.7211 (tp30) REVERT: A 474 MET cc_start: 0.8032 (mmm) cc_final: 0.7242 (mmm) REVERT: A 481 LYS cc_start: 0.8797 (tppp) cc_final: 0.8524 (tppp) REVERT: A 483 GLU cc_start: 0.9166 (tp30) cc_final: 0.8715 (mm-30) REVERT: A 567 THR cc_start: 0.9092 (m) cc_final: 0.8800 (p) REVERT: E 357 ARG cc_start: 0.8842 (ttt180) cc_final: 0.7205 (ptp-170) REVERT: E 396 TYR cc_start: 0.8468 (m-80) cc_final: 0.8256 (m-10) REVERT: E 409 GLN cc_start: 0.9420 (mm110) cc_final: 0.9007 (mp10) REVERT: E 421 TYR cc_start: 0.8632 (m-10) cc_final: 0.8238 (m-10) REVERT: E 442 ASP cc_start: 0.8948 (m-30) cc_final: 0.7905 (m-30) REVERT: E 444 LYS cc_start: 0.8169 (ptmm) cc_final: 0.6619 (mttt) REVERT: E 455 LEU cc_start: 0.9225 (tp) cc_final: 0.8988 (tp) REVERT: E 456 PHE cc_start: 0.8448 (m-80) cc_final: 0.7797 (m-80) REVERT: E 509 ARG cc_start: 0.8419 (mtt180) cc_final: 0.8134 (mmt90) outliers start: 13 outliers final: 8 residues processed: 178 average time/residue: 0.0661 time to fit residues: 15.9362 Evaluate side-chains 162 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.115942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.097370 restraints weight = 37465.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.101850 restraints weight = 15404.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.104782 restraints weight = 8446.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.106744 restraints weight = 5337.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.108076 restraints weight = 3725.846| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6655 Z= 0.170 Angle : 0.719 8.982 9067 Z= 0.360 Chirality : 0.044 0.146 962 Planarity : 0.005 0.051 1166 Dihedral : 5.102 23.834 863 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.62 % Allowed : 19.80 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.30), residues: 789 helix: 0.65 (0.26), residues: 396 sheet: -1.09 (0.70), residues: 58 loop : -1.33 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 393 TYR 0.029 0.002 TYR A 381 PHE 0.041 0.002 PHE A 452 TRP 0.044 0.002 TRP A 477 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 6643) covalent geometry : angle 0.70597 / 0.36 ( 9038) SS BOND : bond 0.00437 / 0.27 ( 7) SS BOND : angle 2.36098 / 1.40 ( 14) hydrogen bonds : bond 0.04357 / 2.87 ( 322) hydrogen bonds : angle 4.92124 / 3.50 ( 916) link_NAG-ASN : bond 0.00270 / 0.17 ( 5) link_NAG-ASN : angle 2.67561 / 1.58 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8764 (t80) cc_final: 0.8448 (t80) REVERT: A 82 MET cc_start: 0.9010 (mtm) cc_final: 0.8492 (ptm) REVERT: A 258 PRO cc_start: 0.7468 (Cg_endo) cc_final: 0.7132 (Cg_exo) REVERT: A 323 MET cc_start: 0.7874 (mmm) cc_final: 0.7165 (mmm) REVERT: A 353 LYS cc_start: 0.8857 (mttt) cc_final: 0.7685 (ttmt) REVERT: A 376 MET cc_start: 0.9180 (mmm) cc_final: 0.8972 (tpt) REVERT: A 398 GLU cc_start: 0.8342 (pt0) cc_final: 0.8043 (pt0) REVERT: A 406 GLU cc_start: 0.8850 (tt0) cc_final: 0.8506 (tt0) REVERT: A 461 TRP cc_start: 0.8213 (m-10) cc_final: 0.7808 (m-10) REVERT: A 481 LYS cc_start: 0.8807 (tppp) cc_final: 0.8551 (tppp) REVERT: A 483 GLU cc_start: 0.9219 (tp30) cc_final: 0.8724 (mm-30) REVERT: A 567 THR cc_start: 0.9154 (m) cc_final: 0.8856 (p) REVERT: E 357 ARG cc_start: 0.8827 (ttt180) cc_final: 0.7300 (mtt180) REVERT: E 396 TYR cc_start: 0.8434 (m-80) cc_final: 0.7983 (m-10) REVERT: E 409 GLN cc_start: 0.9486 (mm110) cc_final: 0.9041 (mp10) REVERT: E 424 LYS cc_start: 0.8785 (tppt) cc_final: 0.8468 (tppt) REVERT: E 442 ASP cc_start: 0.8998 (m-30) cc_final: 0.8083 (m-30) REVERT: E 444 LYS cc_start: 0.8042 (ptmm) cc_final: 0.6564 (mttt) REVERT: E 455 LEU cc_start: 0.9205 (tp) cc_final: 0.8999 (tp) REVERT: E 456 PHE cc_start: 0.8500 (m-80) cc_final: 0.7838 (m-80) outliers start: 17 outliers final: 12 residues processed: 170 average time/residue: 0.0668 time to fit residues: 15.3644 Evaluate side-chains 169 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.115123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.097383 restraints weight = 30390.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.101544 restraints weight = 13598.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104236 restraints weight = 7733.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106109 restraints weight = 5017.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.107414 restraints weight = 3559.936| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6655 Z= 0.173 Angle : 0.737 12.313 9067 Z= 0.365 Chirality : 0.044 0.233 962 Planarity : 0.005 0.050 1166 Dihedral : 5.074 23.353 863 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.77 % Allowed : 20.82 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.30), residues: 789 helix: 0.67 (0.26), residues: 400 sheet: -1.11 (0.70), residues: 58 loop : -1.29 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 403 TYR 0.030 0.002 TYR A 381 PHE 0.036 0.002 PHE A 274 TRP 0.048 0.002 TRP A 477 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 6643) covalent geometry : angle 0.72499 / 0.36 ( 9038) SS BOND : bond 0.00426 / 0.26 ( 7) SS BOND : angle 2.25270 / 1.33 ( 14) hydrogen bonds : bond 0.04320 / 2.85 ( 322) hydrogen bonds : angle 4.84945 / 3.44 ( 916) link_NAG-ASN : bond 0.00297 / 0.18 ( 5) link_NAG-ASN : angle 2.68253 / 1.59 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8797 (t80) cc_final: 0.8508 (t80) REVERT: A 82 MET cc_start: 0.9027 (mtm) cc_final: 0.8519 (ptm) REVERT: A 123 MET cc_start: 0.6321 (mmm) cc_final: 0.5991 (mmm) REVERT: A 187 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7996 (mmmt) REVERT: A 258 PRO cc_start: 0.7424 (Cg_endo) cc_final: 0.7131 (Cg_exo) REVERT: A 297 MET cc_start: 0.8374 (tpp) cc_final: 0.8143 (tpp) REVERT: A 323 MET cc_start: 0.7885 (mmm) cc_final: 0.7320 (mmm) REVERT: A 353 LYS cc_start: 0.8904 (mttt) cc_final: 0.7726 (ttmt) REVERT: A 394 ASN cc_start: 0.8744 (t0) cc_final: 0.8527 (m110) REVERT: A 398 GLU cc_start: 0.8292 (pt0) cc_final: 0.8011 (pt0) REVERT: A 406 GLU cc_start: 0.8859 (tt0) cc_final: 0.8564 (tt0) REVERT: A 461 TRP cc_start: 0.8295 (m-10) cc_final: 0.7938 (m-10) REVERT: A 474 MET cc_start: 0.7869 (mmm) cc_final: 0.7524 (mmm) REVERT: A 481 LYS cc_start: 0.8836 (tppp) cc_final: 0.8576 (tppp) REVERT: A 483 GLU cc_start: 0.9203 (tp30) cc_final: 0.8730 (mm-30) REVERT: A 567 THR cc_start: 0.9154 (m) cc_final: 0.8856 (p) REVERT: E 357 ARG cc_start: 0.8862 (ttt180) cc_final: 0.7225 (ptp-170) REVERT: E 396 TYR cc_start: 0.8475 (m-80) cc_final: 0.7917 (m-10) REVERT: E 409 GLN cc_start: 0.9460 (mm110) cc_final: 0.9054 (mp10) REVERT: E 444 LYS cc_start: 0.8132 (ptmm) cc_final: 0.6665 (mttt) REVERT: E 456 PHE cc_start: 0.8478 (m-80) cc_final: 0.7876 (m-80) REVERT: E 509 ARG cc_start: 0.8470 (mmt90) cc_final: 0.8265 (mmm-85) outliers start: 18 outliers final: 15 residues processed: 161 average time/residue: 0.0648 time to fit residues: 14.2048 Evaluate side-chains 161 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 588 PHE Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.117874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.098329 restraints weight = 42312.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.103128 restraints weight = 16256.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.106301 restraints weight = 8693.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.108390 restraints weight = 5415.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.109865 restraints weight = 3751.695| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6655 Z= 0.149 Angle : 0.745 11.501 9067 Z= 0.367 Chirality : 0.044 0.188 962 Planarity : 0.005 0.051 1166 Dihedral : 4.977 22.641 863 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.47 % Allowed : 21.11 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.31), residues: 789 helix: 0.80 (0.27), residues: 399 sheet: -0.62 (0.73), residues: 53 loop : -1.30 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 403 TYR 0.055 0.002 TYR A 237 PHE 0.026 0.002 PHE A 452 TRP 0.035 0.002 TRP A 477 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 6643) covalent geometry : angle 0.73437 / 0.36 ( 9038) SS BOND : bond 0.00447 / 0.29 ( 7) SS BOND : angle 2.04668 / 1.21 ( 14) hydrogen bonds : bond 0.04324 / 2.95 ( 322) hydrogen bonds : angle 4.82425 / 3.42 ( 916) link_NAG-ASN : bond 0.00265 / 0.16 ( 5) link_NAG-ASN : angle 2.55967 / 1.51 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8784 (t80) cc_final: 0.8437 (t80) REVERT: A 75 GLU cc_start: 0.8541 (pp20) cc_final: 0.7848 (pp20) REVERT: A 76 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8847 (mm-40) REVERT: A 82 MET cc_start: 0.8997 (mtm) cc_final: 0.8588 (ptm) REVERT: A 123 MET cc_start: 0.6630 (mmm) cc_final: 0.6244 (mmm) REVERT: A 187 LYS cc_start: 0.8299 (mmtt) cc_final: 0.8096 (mmmt) REVERT: A 258 PRO cc_start: 0.7395 (Cg_endo) cc_final: 0.7102 (Cg_exo) REVERT: A 297 MET cc_start: 0.8321 (tpp) cc_final: 0.7959 (tpp) REVERT: A 323 MET cc_start: 0.7727 (mmm) cc_final: 0.6734 (mmm) REVERT: A 353 LYS cc_start: 0.8904 (mttt) cc_final: 0.7898 (ttmt) REVERT: A 398 GLU cc_start: 0.8224 (pt0) cc_final: 0.7853 (pt0) REVERT: A 461 TRP cc_start: 0.8251 (m-10) cc_final: 0.7912 (m-10) REVERT: A 483 GLU cc_start: 0.9198 (tp30) cc_final: 0.8710 (mm-30) REVERT: A 567 THR cc_start: 0.9112 (m) cc_final: 0.8819 (p) REVERT: E 357 ARG cc_start: 0.8844 (ttt180) cc_final: 0.7237 (ptp-170) REVERT: E 396 TYR cc_start: 0.8439 (m-80) cc_final: 0.8154 (m-10) REVERT: E 409 GLN cc_start: 0.9448 (mm110) cc_final: 0.9043 (mp10) REVERT: E 442 ASP cc_start: 0.8976 (m-30) cc_final: 0.8151 (m-30) REVERT: E 444 LYS cc_start: 0.8155 (ptmm) cc_final: 0.6665 (mttt) REVERT: E 509 ARG cc_start: 0.8423 (mmt90) cc_final: 0.8165 (mmm-85) outliers start: 16 outliers final: 13 residues processed: 174 average time/residue: 0.0687 time to fit residues: 16.1385 Evaluate side-chains 169 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.116373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.097372 restraints weight = 38143.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.102001 restraints weight = 15476.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105043 restraints weight = 8453.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.107072 restraints weight = 5320.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.108440 restraints weight = 3707.819| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6655 Z= 0.175 Angle : 0.771 11.479 9067 Z= 0.381 Chirality : 0.045 0.166 962 Planarity : 0.006 0.119 1166 Dihedral : 5.076 22.914 863 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.04 % Allowed : 22.42 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.30), residues: 789 helix: 0.67 (0.26), residues: 400 sheet: -0.75 (0.73), residues: 51 loop : -1.32 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 403 TYR 0.038 0.002 TYR E 505 PHE 0.031 0.002 PHE A 274 TRP 0.042 0.002 TRP A 477 HIS 0.007 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 6643) covalent geometry : angle 0.75967 / 0.38 ( 9038) SS BOND : bond 0.00407 / 0.25 ( 7) SS BOND : angle 2.17472 / 1.29 ( 14) hydrogen bonds : bond 0.04415 / 2.99 ( 322) hydrogen bonds : angle 4.85097 / 3.44 ( 916) link_NAG-ASN : bond 0.00281 / 0.17 ( 5) link_NAG-ASN : angle 2.59425 / 1.53 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8791 (t80) cc_final: 0.8378 (t80) REVERT: A 75 GLU cc_start: 0.8515 (pp20) cc_final: 0.7774 (pp20) REVERT: A 76 GLN cc_start: 0.9262 (mm-40) cc_final: 0.8846 (mm-40) REVERT: A 82 MET cc_start: 0.8991 (mtm) cc_final: 0.8518 (ptm) REVERT: A 127 TYR cc_start: 0.7397 (t80) cc_final: 0.6918 (t80) REVERT: A 258 PRO cc_start: 0.7510 (Cg_endo) cc_final: 0.7199 (Cg_exo) REVERT: A 297 MET cc_start: 0.8361 (tpp) cc_final: 0.8134 (tpp) REVERT: A 323 MET cc_start: 0.7770 (mmm) cc_final: 0.6954 (mmm) REVERT: A 353 LYS cc_start: 0.8841 (mttt) cc_final: 0.7790 (ttmt) REVERT: A 360 MET cc_start: 0.8535 (tpt) cc_final: 0.7772 (tpt) REVERT: A 398 GLU cc_start: 0.8265 (pt0) cc_final: 0.8026 (pt0) REVERT: A 461 TRP cc_start: 0.8251 (m-10) cc_final: 0.7962 (m-10) REVERT: A 481 LYS cc_start: 0.8823 (tppp) cc_final: 0.8570 (tttt) REVERT: A 483 GLU cc_start: 0.9197 (tp30) cc_final: 0.8711 (mm-30) REVERT: A 567 THR cc_start: 0.9128 (m) cc_final: 0.8825 (p) REVERT: E 357 ARG cc_start: 0.8847 (ttt180) cc_final: 0.7170 (ptp-170) REVERT: E 409 GLN cc_start: 0.9418 (mm110) cc_final: 0.9105 (mp10) REVERT: E 442 ASP cc_start: 0.9008 (m-30) cc_final: 0.8058 (m-30) REVERT: E 444 LYS cc_start: 0.8205 (ptmm) cc_final: 0.6724 (mttt) REVERT: E 509 ARG cc_start: 0.8442 (mmt90) cc_final: 0.8161 (mmm-85) outliers start: 13 outliers final: 13 residues processed: 162 average time/residue: 0.0690 time to fit residues: 15.0243 Evaluate side-chains 159 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 588 PHE Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 0.0020 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 46 optimal weight: 0.0020 chunk 31 optimal weight: 6.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.118533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.100850 restraints weight = 27288.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.104949 restraints weight = 12607.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.107683 restraints weight = 7287.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.109544 restraints weight = 4757.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.110799 restraints weight = 3397.263| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6655 Z= 0.157 Angle : 0.835 10.980 9067 Z= 0.410 Chirality : 0.046 0.189 962 Planarity : 0.005 0.090 1166 Dihedral : 5.137 34.332 863 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.18 % Allowed : 24.02 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.30), residues: 789 helix: 0.72 (0.26), residues: 390 sheet: -0.59 (0.75), residues: 51 loop : -1.36 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 403 TYR 0.030 0.002 TYR E 505 PHE 0.033 0.002 PHE A 274 TRP 0.044 0.002 TRP A 168 HIS 0.007 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 6643) covalent geometry : angle 0.81952 / 0.40 ( 9038) SS BOND : bond 0.00452 / 0.28 ( 7) SS BOND : angle 3.35066 / 2.02 ( 14) hydrogen bonds : bond 0.04346 / 2.95 ( 322) hydrogen bonds : angle 4.93094 / 3.49 ( 916) link_NAG-ASN : bond 0.00253 / 0.15 ( 5) link_NAG-ASN : angle 2.47430 / 1.46 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8800 (t80) cc_final: 0.8405 (t80) REVERT: A 75 GLU cc_start: 0.8527 (pp20) cc_final: 0.7862 (pp20) REVERT: A 76 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8815 (mm-40) REVERT: A 82 MET cc_start: 0.8996 (mtm) cc_final: 0.8580 (ptm) REVERT: A 127 TYR cc_start: 0.7432 (t80) cc_final: 0.7143 (t80) REVERT: A 258 PRO cc_start: 0.7484 (Cg_endo) cc_final: 0.7182 (Cg_exo) REVERT: A 297 MET cc_start: 0.8330 (tpp) cc_final: 0.7962 (tpp) REVERT: A 323 MET cc_start: 0.7712 (mmm) cc_final: 0.6734 (mmm) REVERT: A 353 LYS cc_start: 0.8720 (mttt) cc_final: 0.7636 (ttmt) REVERT: A 360 MET cc_start: 0.8543 (tpt) cc_final: 0.7849 (tpt) REVERT: A 398 GLU cc_start: 0.8298 (pt0) cc_final: 0.7958 (pt0) REVERT: A 481 LYS cc_start: 0.8814 (tppp) cc_final: 0.8565 (tttt) REVERT: A 483 GLU cc_start: 0.9200 (tp30) cc_final: 0.8697 (mm-30) REVERT: A 543 ASP cc_start: 0.9231 (t0) cc_final: 0.9021 (t0) REVERT: A 567 THR cc_start: 0.9110 (m) cc_final: 0.8817 (p) REVERT: E 357 ARG cc_start: 0.8831 (ttt180) cc_final: 0.7011 (ptp-170) REVERT: E 396 TYR cc_start: 0.8465 (m-80) cc_final: 0.8044 (m-10) REVERT: E 409 GLN cc_start: 0.9408 (mm110) cc_final: 0.9084 (mp10) REVERT: E 442 ASP cc_start: 0.8997 (m-30) cc_final: 0.8152 (m-30) REVERT: E 444 LYS cc_start: 0.8177 (ptmm) cc_final: 0.6712 (mttt) REVERT: E 509 ARG cc_start: 0.8365 (mmt90) cc_final: 0.8084 (mmm-85) outliers start: 14 outliers final: 11 residues processed: 163 average time/residue: 0.0699 time to fit residues: 15.4144 Evaluate side-chains 162 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 588 PHE Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.118383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.100720 restraints weight = 27863.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.104899 restraints weight = 12662.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.107641 restraints weight = 7210.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.109509 restraints weight = 4672.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.110770 restraints weight = 3311.924| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6655 Z= 0.163 Angle : 0.820 11.084 9067 Z= 0.407 Chirality : 0.046 0.202 962 Planarity : 0.005 0.052 1166 Dihedral : 5.135 31.946 863 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.04 % Allowed : 24.45 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.30), residues: 789 helix: 0.68 (0.26), residues: 391 sheet: -0.48 (0.75), residues: 52 loop : -1.46 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 219 TYR 0.029 0.002 TYR A 381 PHE 0.032 0.002 PHE A 274 TRP 0.059 0.002 TRP A 168 HIS 0.007 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 6643) covalent geometry : angle 0.80644 / 0.40 ( 9038) SS BOND : bond 0.00504 / 0.32 ( 7) SS BOND : angle 3.11159 / 1.90 ( 14) hydrogen bonds : bond 0.04346 / 2.96 ( 322) hydrogen bonds : angle 4.92878 / 3.50 ( 916) link_NAG-ASN : bond 0.00256 / 0.16 ( 5) link_NAG-ASN : angle 2.44699 / 1.45 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1207.71 seconds wall clock time: 21 minutes 37.77 seconds (1297.77 seconds total)