Starting phenix.real_space_refine on Tue Feb 3 19:38:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fdg_31542/02_2026/7fdg_31542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdg_31542/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/7fdg_31542/02_2026/7fdg_31542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdg_31542/02_2026/7fdg_31542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fdg_31542/02_2026/7fdg_31542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdg_31542/02_2026/7fdg_31542.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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 dihedrals: 12 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.86, per 1000 atoms: 0.44 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: 0.69 Conformation dependent library (CDL) restraints added in 456.4 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: 0.21 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: 1.01 Time building geometry restraints manager: 0.89 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: 3501 17.31 - 34.63: 354 34.63 - 51.94: 81 51.94 - 69.26: 29 69.26 - 86.57: 13 Dihedral angle restraints: 3978 sinusoidal: 1649 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 3975 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: 2.260 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 16.003 86.573 2465 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 covalent geometry : bond 0.00656 ( 6643) covalent geometry : angle 0.84766 ( 9038) SS BOND : bond 0.00709 ( 7) SS BOND : angle 3.08745 ( 14) hydrogen bonds : bond 0.14417 ( 322) hydrogen bonds : angle 6.69268 ( 916) link_NAG-ASN : bond 0.00527 ( 5) link_NAG-ASN : angle 3.92781 ( 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 : 0.247 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: 0.0886 time to fit residues: 22.4687 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 : 0.253 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3812 r_free = 0.3812 target = 0.112027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092515 restraints weight = 51151.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.097367 restraints weight = 17574.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100510 restraints weight = 9038.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102632 restraints weight = 5544.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104113 restraints weight = 3771.261| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 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 = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2023 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= 0.198 Angle : 0.776 8.700 9067 Z= 0.395 Chirality : 0.048 0.217 962 Planarity : 0.006 0.051 1166 Dihedral : 7.803 59.005 968 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.89 % Allowed : 16.01 % Favored : 82.10 % 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: -1.52 (0.28), residues: 789 helix: -0.20 (0.25), residues: 378 sheet: -1.67 (0.68), residues: 51 loop : -1.76 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 219 TYR 0.028 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 covalent geometry : bond 0.00428 ( 6643) covalent geometry : angle 0.75424 ( 9038) SS BOND : bond 0.00633 ( 7) SS BOND : angle 2.73984 ( 14) hydrogen bonds : bond 0.05142 ( 322) hydrogen bonds : angle 5.49609 ( 916) link_NAG-ASN : bond 0.00407 ( 5) link_NAG-ASN : angle 3.82343 ( 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 184 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.242 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: symmetry clash REVERT: A 29 LEU cc_start: 0.9579 (mt) cc_final: 0.9337 (mt) REVERT: A 76 GLN cc_start: 0.9375 (mm-40) cc_final: 0.8583 (mm-40) REVERT: A 127 TYR cc_start: 0.7014 (t80) cc_final: 0.6779 (t80) REVERT: A 249 MET cc_start: 0.7950 (ttp) cc_final: 0.7672 (ttp) REVERT: A 258 PRO cc_start: 0.7828 (Cg_endo) cc_final: 0.7301 (Cg_exo) REVERT: A 275 TRP cc_start: 0.8812 (m-10) cc_final: 0.8577 (m-10) REVERT: A 323 MET cc_start: 0.8221 (mmm) cc_final: 0.7205 (mmm) REVERT: A 332 MET cc_start: 0.8185 (tpt) cc_final: 0.7968 (tmm) REVERT: A 340 GLN cc_start: 0.7165 (pt0) cc_final: 0.6959 (tp-100) REVERT: A 353 LYS cc_start: 0.9057 (tttt) cc_final: 0.7942 (ttmt) REVERT: A 360 MET cc_start: 0.8003 (tmm) cc_final: 0.7693 (tpt) REVERT: A 392 LEU cc_start: 0.9324 (mm) cc_final: 0.9055 (mm) REVERT: A 398 GLU cc_start: 0.8359 (pt0) cc_final: 0.8106 (pt0) REVERT: A 455 MET cc_start: 0.9173 (tmm) cc_final: 0.8924 (tmm) REVERT: A 481 LYS cc_start: 0.8947 (tppp) cc_final: 0.8525 (ttpt) REVERT: A 483 GLU cc_start: 0.9219 (tp30) cc_final: 0.8688 (mm-30) REVERT: A 485 VAL cc_start: 0.8544 (t) cc_final: 0.8317 (t) REVERT: A 503 LEU cc_start: 0.8784 (tp) cc_final: 0.8573 (tp) REVERT: E 357 ARG cc_start: 0.8623 (ttt180) cc_final: 0.7245 (mtt180) REVERT: E 424 LYS cc_start: 0.9024 (tppt) cc_final: 0.8823 (tppt) REVERT: E 442 ASP cc_start: 0.9009 (m-30) cc_final: 0.8309 (m-30) REVERT: E 444 LYS cc_start: 0.7750 (ptmm) cc_final: 0.6144 (mttt) REVERT: E 455 LEU cc_start: 0.9293 (tp) cc_final: 0.9040 (tp) outliers start: 11 outliers final: 7 residues processed: 179 average time/residue: 0.0731 time to fit residues: 17.7267 Evaluate side-chains 153 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 40.0000 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 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 = 0.3871 r_free = 0.3871 target = 0.116057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.097676 restraints weight = 27951.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.101867 restraints weight = 12487.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104655 restraints weight = 7145.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.106513 restraints weight = 4659.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.107797 restraints weight = 3349.572| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- 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 = 0.34 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 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2761 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= 0.157 Angle : 0.724 7.640 9067 Z= 0.364 Chirality : 0.045 0.162 962 Planarity : 0.005 0.050 1166 Dihedral : 6.977 55.266 968 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.04 % Allowed : 17.76 % Favored : 80.20 % 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: -0.85 (0.29), residues: 789 helix: 0.43 (0.26), residues: 378 sheet: -1.64 (0.64), residues: 62 loop : -1.43 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.024 0.002 TYR A 521 PHE 0.028 0.002 PHE A 230 TRP 0.019 0.001 TRP A 477 HIS 0.006 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6643) covalent geometry : angle 0.70547 ( 9038) SS BOND : bond 0.00643 ( 7) SS BOND : angle 2.51258 ( 14) hydrogen bonds : bond 0.04644 ( 322) hydrogen bonds : angle 5.14640 ( 916) link_NAG-ASN : bond 0.00291 ( 5) link_NAG-ASN : angle 3.29522 ( 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 181 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.167 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: 0.8776 (t80) cc_final: 0.8567 (t80) REVERT: A 76 GLN cc_start: 0.9335 (mm-40) cc_final: 0.8790 (mm-40) REVERT: A 82 MET cc_start: 0.9210 (mtm) cc_final: 0.9003 (mtm) REVERT: A 127 TYR cc_start: 0.7059 (t80) cc_final: 0.6765 (t80) REVERT: A 249 MET cc_start: 0.7922 (ttp) cc_final: 0.7656 (ttp) REVERT: A 258 PRO cc_start: 0.7877 (Cg_endo) cc_final: 0.7433 (Cg_exo) REVERT: A 275 TRP cc_start: 0.8751 (m-10) cc_final: 0.8467 (m-10) REVERT: A 323 MET cc_start: 0.7886 (mmm) cc_final: 0.6832 (mmm) REVERT: A 332 MET cc_start: 0.8142 (tpt) cc_final: 0.7898 (tpt) REVERT: A 353 LYS cc_start: 0.8984 (tttt) cc_final: 0.7836 (ttmt) REVERT: A 360 MET cc_start: 0.7957 (mmm) cc_final: 0.7223 (tpt) REVERT: A 376 MET cc_start: 0.9255 (mmm) cc_final: 0.8912 (tpt) REVERT: A 398 GLU cc_start: 0.8348 (pt0) cc_final: 0.8035 (pt0) REVERT: A 406 GLU cc_start: 0.8842 (tt0) cc_final: 0.8040 (tt0) REVERT: A 452 PHE cc_start: 0.8612 (t80) cc_final: 0.8311 (t80) REVERT: A 477 TRP cc_start: 0.6707 (t-100) cc_final: 0.6269 (t-100) REVERT: A 481 LYS cc_start: 0.8897 (tppp) cc_final: 0.8491 (ttpt) REVERT: A 483 GLU cc_start: 0.9213 (tp30) cc_final: 0.8672 (mm-30) REVERT: A 503 LEU cc_start: 0.8885 (tp) cc_final: 0.8667 (tp) REVERT: A 567 THR cc_start: 0.9144 (m) cc_final: 0.8859 (p) REVERT: E 335 LEU cc_start: 0.7661 (mm) cc_final: 0.7357 (mm) REVERT: E 357 ARG cc_start: 0.8515 (ttt180) cc_final: 0.7186 (mtt180) REVERT: E 421 TYR cc_start: 0.8668 (m-10) cc_final: 0.8456 (m-10) REVERT: E 444 LYS cc_start: 0.7859 (ptmm) cc_final: 0.6397 (mttt) REVERT: E 455 LEU cc_start: 0.9241 (tp) cc_final: 0.8999 (tp) REVERT: E 456 PHE cc_start: 0.8412 (m-80) cc_final: 0.7822 (m-80) REVERT: E 509 ARG cc_start: 0.8417 (mtt180) cc_final: 0.7968 (mmm-85) outliers start: 12 outliers final: 7 residues processed: 175 average time/residue: 0.0714 time to fit residues: 16.8265 Evaluate side-chains 162 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 513 ILE Chi-restraints excluded: chain A residue 530 CYS 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: 0.9990 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.113588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.094666 restraints weight = 36246.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099188 restraints weight = 14879.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.102210 restraints weight = 8176.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.104217 restraints weight = 5171.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.105584 restraints weight = 3611.625| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6655 Z= 0.169 Angle : 0.733 9.260 9067 Z= 0.370 Chirality : 0.045 0.192 962 Planarity : 0.005 0.048 1166 Dihedral : 6.726 47.796 968 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.77 % Allowed : 18.78 % Favored : 78.46 % 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: -0.63 (0.29), residues: 789 helix: 0.59 (0.25), residues: 383 sheet: -1.41 (0.66), residues: 60 loop : -1.36 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 393 TYR 0.030 0.002 TYR A 381 PHE 0.025 0.002 PHE A 230 TRP 0.026 0.002 TRP A 477 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 6643) covalent geometry : angle 0.72098 ( 9038) SS BOND : bond 0.00503 ( 7) SS BOND : angle 2.25292 ( 14) hydrogen bonds : bond 0.04568 ( 322) hydrogen bonds : angle 5.04597 ( 916) link_NAG-ASN : bond 0.00265 ( 5) link_NAG-ASN : angle 2.64520 ( 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 186 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.288 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: 0.8818 (t80) cc_final: 0.8454 (t80) REVERT: A 75 GLU cc_start: 0.8546 (pp20) cc_final: 0.8003 (pp20) REVERT: A 76 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8865 (mm-40) REVERT: A 82 MET cc_start: 0.9257 (mtm) cc_final: 0.8530 (mtm) REVERT: A 127 TYR cc_start: 0.7074 (t80) cc_final: 0.6825 (t80) REVERT: A 249 MET cc_start: 0.7842 (ttp) cc_final: 0.7622 (ttp) REVERT: A 258 PRO cc_start: 0.7841 (Cg_endo) cc_final: 0.7405 (Cg_exo) REVERT: A 323 MET cc_start: 0.7840 (mmm) cc_final: 0.7003 (mmm) REVERT: A 353 LYS cc_start: 0.8982 (mttt) cc_final: 0.7925 (ttmt) REVERT: A 376 MET cc_start: 0.9183 (mmm) cc_final: 0.8843 (tpt) REVERT: A 392 LEU cc_start: 0.9454 (mm) cc_final: 0.8990 (mm) REVERT: A 398 GLU cc_start: 0.8290 (pt0) cc_final: 0.8034 (pt0) REVERT: A 477 TRP cc_start: 0.6627 (t-100) cc_final: 0.6222 (t-100) REVERT: A 481 LYS cc_start: 0.8788 (tppp) cc_final: 0.8441 (ttpt) REVERT: A 483 GLU cc_start: 0.9221 (tp30) cc_final: 0.8714 (mm-30) REVERT: A 567 THR cc_start: 0.9151 (m) cc_final: 0.8894 (p) REVERT: E 335 LEU cc_start: 0.7808 (mm) cc_final: 0.7518 (mm) REVERT: E 357 ARG cc_start: 0.8482 (ttt180) cc_final: 0.7289 (mtt180) REVERT: E 396 TYR cc_start: 0.8644 (m-80) cc_final: 0.8152 (m-10) REVERT: E 409 GLN cc_start: 0.9468 (mm110) cc_final: 0.9000 (mp10) REVERT: E 421 TYR cc_start: 0.8609 (m-10) cc_final: 0.8255 (m-10) REVERT: E 423 TYR cc_start: 0.8676 (t80) cc_final: 0.7569 (t80) REVERT: E 442 ASP cc_start: 0.8975 (m-30) cc_final: 0.8057 (m-30) REVERT: E 444 LYS cc_start: 0.8013 (ptmm) cc_final: 0.6522 (mttt) REVERT: E 455 LEU cc_start: 0.9220 (tp) cc_final: 0.9013 (tp) REVERT: E 509 ARG cc_start: 0.8395 (mtt180) cc_final: 0.7781 (mmm-85) outliers start: 18 outliers final: 14 residues processed: 178 average time/residue: 0.0790 time to fit residues: 18.8511 Evaluate side-chains 173 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 241 HIS Chi-restraints excluded: chain A residue 281 LEU 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 398 ASP 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: 6.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 394 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.117803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.098533 restraints weight = 34158.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.102956 restraints weight = 14371.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.105911 restraints weight = 8019.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.107922 restraints weight = 5152.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.109241 restraints weight = 3651.543| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 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 = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6655 Z= 0.156 Angle : 0.714 9.364 9067 Z= 0.358 Chirality : 0.044 0.142 962 Planarity : 0.005 0.050 1166 Dihedral : 6.204 42.929 968 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.04 % Allowed : 21.25 % Favored : 76.71 % 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: -0.46 (0.30), residues: 789 helix: 0.71 (0.26), residues: 386 sheet: -1.16 (0.70), residues: 58 loop : -1.29 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 393 TYR 0.028 0.002 TYR A 381 PHE 0.033 0.002 PHE A 274 TRP 0.025 0.002 TRP A 477 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6643) covalent geometry : angle 0.70181 ( 9038) SS BOND : bond 0.00479 ( 7) SS BOND : angle 2.18311 ( 14) hydrogen bonds : bond 0.04332 ( 322) hydrogen bonds : angle 4.95381 ( 916) link_NAG-ASN : bond 0.00236 ( 5) link_NAG-ASN : angle 2.67298 ( 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 178 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.249 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: 0.8793 (t80) cc_final: 0.8420 (t80) REVERT: A 75 GLU cc_start: 0.8545 (pp20) cc_final: 0.8028 (pp20) REVERT: A 76 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8889 (mm-40) REVERT: A 82 MET cc_start: 0.9236 (mtm) cc_final: 0.8622 (mtm) REVERT: A 127 TYR cc_start: 0.7042 (t80) cc_final: 0.6839 (t80) REVERT: A 258 PRO cc_start: 0.7714 (Cg_endo) cc_final: 0.7300 (Cg_exo) REVERT: A 323 MET cc_start: 0.7866 (mmm) cc_final: 0.6899 (mmm) REVERT: A 353 LYS cc_start: 0.8819 (mttt) cc_final: 0.7712 (ttmt) REVERT: A 376 MET cc_start: 0.9114 (mmm) cc_final: 0.8854 (tpt) REVERT: A 398 GLU cc_start: 0.8307 (pt0) cc_final: 0.8030 (pt0) REVERT: A 406 GLU cc_start: 0.8768 (tt0) cc_final: 0.8419 (tt0) REVERT: A 461 TRP cc_start: 0.8295 (m-10) cc_final: 0.7977 (m-10) REVERT: A 481 LYS cc_start: 0.8744 (tppp) cc_final: 0.8498 (tppp) REVERT: A 483 GLU cc_start: 0.9234 (tp30) cc_final: 0.8635 (mm-30) REVERT: A 499 ASP cc_start: 0.8495 (m-30) cc_final: 0.8040 (t0) REVERT: A 567 THR cc_start: 0.9137 (m) cc_final: 0.8838 (p) REVERT: E 335 LEU cc_start: 0.7613 (mm) cc_final: 0.7330 (mm) REVERT: E 357 ARG cc_start: 0.8845 (ttt180) cc_final: 0.7231 (ptp-170) REVERT: E 396 TYR cc_start: 0.8479 (m-80) cc_final: 0.8173 (m-10) REVERT: E 409 GLN cc_start: 0.9450 (mm110) cc_final: 0.9017 (mp10) REVERT: E 423 TYR cc_start: 0.8696 (t80) cc_final: 0.7557 (t80) REVERT: E 442 ASP cc_start: 0.8974 (m-30) cc_final: 0.7915 (m-30) REVERT: E 444 LYS cc_start: 0.8103 (ptmm) cc_final: 0.6575 (mttt) REVERT: E 456 PHE cc_start: 0.8466 (m-80) cc_final: 0.7822 (m-80) REVERT: E 509 ARG cc_start: 0.8369 (mtt180) cc_final: 0.7725 (mmm-85) outliers start: 13 outliers final: 11 residues processed: 171 average time/residue: 0.0685 time to fit residues: 15.8503 Evaluate side-chains 168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 24 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 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 = 0.3850 r_free = 0.3850 target = 0.113711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.095574 restraints weight = 37617.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099923 restraints weight = 14987.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.102795 restraints weight = 8144.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104720 restraints weight = 5121.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.106034 restraints weight = 3559.519| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6655 Z= 0.231 Angle : 0.764 11.055 9067 Z= 0.386 Chirality : 0.046 0.246 962 Planarity : 0.005 0.049 1166 Dihedral : 6.412 45.537 968 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.06 % Allowed : 20.09 % Favored : 76.86 % 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: -0.73 (0.30), residues: 789 helix: 0.49 (0.25), residues: 401 sheet: -1.31 (0.68), residues: 60 loop : -1.52 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 273 TYR 0.031 0.002 TYR A 381 PHE 0.040 0.002 PHE A 452 TRP 0.033 0.002 TRP A 477 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 6643) covalent geometry : angle 0.74985 ( 9038) SS BOND : bond 0.00451 ( 7) SS BOND : angle 2.45222 ( 14) hydrogen bonds : bond 0.04573 ( 322) hydrogen bonds : angle 5.03645 ( 916) link_NAG-ASN : bond 0.00363 ( 5) link_NAG-ASN : angle 2.85119 ( 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 175 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.251 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: 0.8841 (t80) cc_final: 0.8393 (t80) REVERT: A 75 GLU cc_start: 0.8527 (pp20) cc_final: 0.7932 (pp20) REVERT: A 76 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8887 (mm-40) REVERT: A 127 TYR cc_start: 0.7047 (t80) cc_final: 0.6793 (t80) REVERT: A 258 PRO cc_start: 0.7462 (Cg_endo) cc_final: 0.7124 (Cg_exo) REVERT: A 323 MET cc_start: 0.7945 (mmm) cc_final: 0.7255 (mmm) REVERT: A 353 LYS cc_start: 0.8965 (mttt) cc_final: 0.7808 (ttmt) REVERT: A 376 MET cc_start: 0.9224 (mmm) cc_final: 0.8845 (tpt) REVERT: A 392 LEU cc_start: 0.9154 (mm) cc_final: 0.8927 (mm) REVERT: A 398 GLU cc_start: 0.8288 (pt0) cc_final: 0.8003 (pt0) REVERT: A 430 GLU cc_start: 0.7466 (tp30) cc_final: 0.7188 (tp30) REVERT: A 461 TRP cc_start: 0.8239 (m-10) cc_final: 0.7968 (m-10) REVERT: A 481 LYS cc_start: 0.8791 (tppp) cc_final: 0.8479 (ttpt) REVERT: A 483 GLU cc_start: 0.9183 (tp30) cc_final: 0.8722 (mm-30) REVERT: A 499 ASP cc_start: 0.8553 (m-30) cc_final: 0.8027 (t0) REVERT: A 567 THR cc_start: 0.9164 (m) cc_final: 0.8892 (p) REVERT: E 357 ARG cc_start: 0.8896 (ttt180) cc_final: 0.7255 (ptp-170) REVERT: E 409 GLN cc_start: 0.9459 (mm110) cc_final: 0.9049 (mp10) REVERT: E 424 LYS cc_start: 0.8873 (tppt) cc_final: 0.8555 (tppt) REVERT: E 442 ASP cc_start: 0.8998 (m-30) cc_final: 0.7926 (m-30) REVERT: E 444 LYS cc_start: 0.8127 (ptmm) cc_final: 0.6632 (mttt) REVERT: E 509 ARG cc_start: 0.8495 (mtt180) cc_final: 0.7860 (mmm-85) outliers start: 20 outliers final: 13 residues processed: 166 average time/residue: 0.0697 time to fit residues: 15.6487 Evaluate side-chains 160 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 236 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 503 LEU 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 481 ASN 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: 4.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN 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 = 0.3922 r_free = 0.3922 target = 0.119709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.100957 restraints weight = 29803.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105294 restraints weight = 13080.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.108170 restraints weight = 7384.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.110135 restraints weight = 4773.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.111447 restraints weight = 3385.319| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4069 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= 0.139 Angle : 0.743 9.155 9067 Z= 0.366 Chirality : 0.044 0.212 962 Planarity : 0.005 0.061 1166 Dihedral : 5.977 41.601 968 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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 : 0.13 % 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: -0.48 (0.30), residues: 789 helix: 0.67 (0.26), residues: 399 sheet: -1.11 (0.70), residues: 58 loop : -1.36 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.029 0.002 TYR A 381 PHE 0.042 0.002 PHE A 452 TRP 0.044 0.002 TRP A 477 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6643) covalent geometry : angle 0.72639 ( 9038) SS BOND : bond 0.00575 ( 7) SS BOND : angle 2.96265 ( 14) hydrogen bonds : bond 0.04159 ( 322) hydrogen bonds : angle 4.85653 ( 916) link_NAG-ASN : bond 0.00216 ( 5) link_NAG-ASN : angle 2.68101 ( 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 184 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8792 (t80) cc_final: 0.8424 (t80) REVERT: A 75 GLU cc_start: 0.8539 (pp20) cc_final: 0.7988 (pp20) REVERT: A 76 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8887 (mm-40) REVERT: A 127 TYR cc_start: 0.7116 (t80) cc_final: 0.6844 (t80) REVERT: A 183 TYR cc_start: 0.9070 (t80) cc_final: 0.8607 (t80) REVERT: A 258 PRO cc_start: 0.7449 (Cg_endo) cc_final: 0.7165 (Cg_exo) REVERT: A 297 MET cc_start: 0.8411 (tpp) cc_final: 0.8001 (tpp) REVERT: A 323 MET cc_start: 0.7740 (mmm) cc_final: 0.7133 (mmm) REVERT: A 353 LYS cc_start: 0.8839 (mttt) cc_final: 0.7678 (ttmt) REVERT: A 376 MET cc_start: 0.9075 (mmm) cc_final: 0.8840 (tpt) REVERT: A 398 GLU cc_start: 0.8116 (pt0) cc_final: 0.7761 (pt0) REVERT: A 406 GLU cc_start: 0.8832 (tt0) cc_final: 0.8488 (tt0) REVERT: A 461 TRP cc_start: 0.8203 (m-10) cc_final: 0.7810 (m-10) REVERT: A 481 LYS cc_start: 0.8783 (tppp) cc_final: 0.8471 (tppt) REVERT: A 483 GLU cc_start: 0.9198 (tp30) cc_final: 0.8713 (mm-30) REVERT: A 499 ASP cc_start: 0.8372 (m-30) cc_final: 0.7888 (t70) REVERT: A 515 TYR cc_start: 0.8548 (m-10) cc_final: 0.7802 (m-10) REVERT: A 518 ARG cc_start: 0.8826 (tmm-80) cc_final: 0.8439 (tmm-80) REVERT: A 567 THR cc_start: 0.9113 (m) cc_final: 0.8820 (p) REVERT: E 338 PHE cc_start: 0.8538 (m-80) cc_final: 0.8330 (m-80) REVERT: E 357 ARG cc_start: 0.8801 (ttt180) cc_final: 0.6939 (ptp-170) REVERT: E 360 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8606 (p0) REVERT: E 361 CYS cc_start: 0.6401 (OUTLIER) cc_final: 0.5961 (p) REVERT: E 409 GLN cc_start: 0.9482 (mm110) cc_final: 0.9034 (mp10) REVERT: E 442 ASP cc_start: 0.8978 (m-30) cc_final: 0.7973 (m-30) REVERT: E 444 LYS cc_start: 0.8130 (ptmm) cc_final: 0.6656 (mttt) REVERT: E 473 TYR cc_start: 0.8732 (t80) cc_final: 0.8279 (t80) REVERT: E 509 ARG cc_start: 0.8287 (mtt180) cc_final: 0.7724 (mmm-85) outliers start: 16 outliers final: 9 residues processed: 177 average time/residue: 0.0581 time to fit residues: 13.9047 Evaluate side-chains 169 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 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 361 CYS 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: 5.9990 chunk 58 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 394 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.117566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.098118 restraints weight = 42295.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102941 restraints weight = 16071.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.106129 restraints weight = 8535.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.108275 restraints weight = 5263.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.109738 restraints weight = 3599.616| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6655 Z= 0.157 Angle : 0.769 9.653 9067 Z= 0.380 Chirality : 0.045 0.170 962 Planarity : 0.005 0.057 1166 Dihedral : 5.882 40.029 968 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.18 % Allowed : 23.44 % Favored : 74.38 % 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: -0.52 (0.30), residues: 789 helix: 0.57 (0.26), residues: 406 sheet: -0.81 (0.72), residues: 55 loop : -1.38 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 559 TYR 0.055 0.002 TYR A 237 PHE 0.044 0.002 PHE A 452 TRP 0.056 0.002 TRP A 477 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6643) covalent geometry : angle 0.75428 ( 9038) SS BOND : bond 0.00466 ( 7) SS BOND : angle 2.87397 ( 14) hydrogen bonds : bond 0.04330 ( 322) hydrogen bonds : angle 4.90581 ( 916) link_NAG-ASN : bond 0.00230 ( 5) link_NAG-ASN : angle 2.59287 ( 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 172 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8811 (t80) cc_final: 0.8305 (t80) REVERT: A 75 GLU cc_start: 0.8494 (pp20) cc_final: 0.7734 (pp20) REVERT: A 76 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8860 (mm110) REVERT: A 127 TYR cc_start: 0.7015 (t80) cc_final: 0.6755 (t80) REVERT: A 258 PRO cc_start: 0.7477 (Cg_endo) cc_final: 0.7203 (Cg_exo) REVERT: A 297 MET cc_start: 0.8415 (tpp) cc_final: 0.7997 (tpp) REVERT: A 323 MET cc_start: 0.7857 (mmm) cc_final: 0.7052 (mmm) REVERT: A 353 LYS cc_start: 0.8878 (mttt) cc_final: 0.7719 (ttmt) REVERT: A 376 MET cc_start: 0.9072 (mmm) cc_final: 0.8815 (tpt) REVERT: A 398 GLU cc_start: 0.8189 (pt0) cc_final: 0.7897 (pt0) REVERT: A 461 TRP cc_start: 0.8158 (m-10) cc_final: 0.7769 (m-10) REVERT: A 481 LYS cc_start: 0.8819 (tppp) cc_final: 0.8495 (tppt) REVERT: A 483 GLU cc_start: 0.9171 (tp30) cc_final: 0.8687 (mm-30) REVERT: A 499 ASP cc_start: 0.8393 (m-30) cc_final: 0.7789 (t70) REVERT: A 567 THR cc_start: 0.9103 (m) cc_final: 0.8818 (p) REVERT: E 357 ARG cc_start: 0.8820 (ttt180) cc_final: 0.7165 (mtt180) REVERT: E 409 GLN cc_start: 0.9458 (mm110) cc_final: 0.9042 (mp10) REVERT: E 442 ASP cc_start: 0.9013 (m-30) cc_final: 0.8228 (m-30) REVERT: E 444 LYS cc_start: 0.8193 (ptmm) cc_final: 0.6705 (mttt) REVERT: E 473 TYR cc_start: 0.8732 (t80) cc_final: 0.8293 (t80) outliers start: 14 outliers final: 10 residues processed: 167 average time/residue: 0.0655 time to fit residues: 15.1131 Evaluate side-chains 160 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.116006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096951 restraints weight = 38366.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.101604 restraints weight = 15663.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.104711 restraints weight = 8531.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.106746 restraints weight = 5343.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.108179 restraints weight = 3701.837| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- 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 = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6655 Z= 0.175 Angle : 0.792 11.294 9067 Z= 0.390 Chirality : 0.046 0.158 962 Planarity : 0.005 0.056 1166 Dihedral : 5.875 40.575 968 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.62 % Allowed : 23.14 % Favored : 74.24 % 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: -0.59 (0.30), residues: 789 helix: 0.51 (0.26), residues: 406 sheet: -0.77 (0.73), residues: 57 loop : -1.44 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 559 TYR 0.028 0.002 TYR A 381 PHE 0.040 0.002 PHE A 452 TRP 0.051 0.002 TRP A 477 HIS 0.007 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6643) covalent geometry : angle 0.77861 ( 9038) SS BOND : bond 0.00741 ( 7) SS BOND : angle 2.77229 ( 14) hydrogen bonds : bond 0.04425 ( 322) hydrogen bonds : angle 4.92289 ( 916) link_NAG-ASN : bond 0.00255 ( 5) link_NAG-ASN : angle 2.60166 ( 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: 17 poor density : 150 time to evaluate : 0.236 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 127 TYR cc_start: 0.7046 (t80) cc_final: 0.6798 (t80) REVERT: A 258 PRO cc_start: 0.7522 (Cg_endo) cc_final: 0.7218 (Cg_exo) REVERT: A 323 MET cc_start: 0.7869 (mmm) cc_final: 0.7342 (mmm) REVERT: A 353 LYS cc_start: 0.8914 (mttt) cc_final: 0.7755 (ttmt) REVERT: A 398 GLU cc_start: 0.8299 (pt0) cc_final: 0.7992 (pt0) REVERT: A 461 TRP cc_start: 0.8168 (m-10) cc_final: 0.7793 (m-10) REVERT: A 481 LYS cc_start: 0.8855 (tppp) cc_final: 0.8543 (ttpt) REVERT: A 483 GLU cc_start: 0.9165 (tp30) cc_final: 0.8680 (mm-30) REVERT: A 499 ASP cc_start: 0.8379 (m-30) cc_final: 0.7829 (t70) REVERT: A 567 THR cc_start: 0.9125 (m) cc_final: 0.8843 (p) REVERT: E 338 PHE cc_start: 0.8087 (m-80) cc_final: 0.7776 (m-80) REVERT: E 357 ARG cc_start: 0.8781 (ttt180) cc_final: 0.7097 (mtt180) REVERT: E 409 GLN cc_start: 0.9431 (mm110) cc_final: 0.9036 (mp10) REVERT: E 442 ASP cc_start: 0.8987 (m-30) cc_final: 0.8084 (m-30) REVERT: E 444 LYS cc_start: 0.8226 (ptmm) cc_final: 0.6747 (mttt) REVERT: E 473 TYR cc_start: 0.8769 (t80) cc_final: 0.8353 (t80) REVERT: E 509 ARG cc_start: 0.8493 (mmt90) cc_final: 0.8071 (mmm-85) outliers start: 17 outliers final: 16 residues processed: 162 average time/residue: 0.0666 time to fit residues: 14.6436 Evaluate side-chains 163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 491 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 A residue 588 PHE Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 361 CYS 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: 2.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 25 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** E 394 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.118737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101081 restraints weight = 27467.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105276 restraints weight = 12701.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.108028 restraints weight = 7289.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.109920 restraints weight = 4728.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.111167 restraints weight = 3347.310| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6655 Z= 0.150 Angle : 0.803 10.947 9067 Z= 0.395 Chirality : 0.046 0.161 962 Planarity : 0.005 0.055 1166 Dihedral : 5.743 39.057 968 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.33 % Allowed : 23.58 % Favored : 74.09 % 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: -0.66 (0.30), residues: 789 helix: 0.46 (0.26), residues: 406 sheet: -0.88 (0.72), residues: 59 loop : -1.46 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 403 TYR 0.027 0.002 TYR A 381 PHE 0.040 0.002 PHE A 452 TRP 0.049 0.002 TRP A 477 HIS 0.009 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6643) covalent geometry : angle 0.79130 ( 9038) SS BOND : bond 0.00654 ( 7) SS BOND : angle 2.64632 ( 14) hydrogen bonds : bond 0.04393 ( 322) hydrogen bonds : angle 4.98877 ( 916) link_NAG-ASN : bond 0.00256 ( 5) link_NAG-ASN : angle 2.48869 ( 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 172 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.7130 (t80) cc_final: 0.6910 (t80) REVERT: A 258 PRO cc_start: 0.7479 (Cg_endo) cc_final: 0.7184 (Cg_exo) REVERT: A 297 MET cc_start: 0.8393 (tpp) cc_final: 0.7987 (tpp) REVERT: A 353 LYS cc_start: 0.8897 (mttt) cc_final: 0.7791 (ttmt) REVERT: A 360 MET cc_start: 0.8213 (tpt) cc_final: 0.7438 (tpt) REVERT: A 398 GLU cc_start: 0.8166 (pt0) cc_final: 0.7839 (pt0) REVERT: A 406 GLU cc_start: 0.8704 (tt0) cc_final: 0.8423 (tt0) REVERT: A 461 TRP cc_start: 0.8159 (m-10) cc_final: 0.7777 (m-10) REVERT: A 481 LYS cc_start: 0.8844 (tppp) cc_final: 0.8528 (tppt) REVERT: A 483 GLU cc_start: 0.9146 (tp30) cc_final: 0.8669 (mm-30) REVERT: A 499 ASP cc_start: 0.8380 (m-30) cc_final: 0.7743 (t0) REVERT: A 567 THR cc_start: 0.9094 (m) cc_final: 0.8807 (p) REVERT: E 357 ARG cc_start: 0.8806 (ttt180) cc_final: 0.7034 (mtt180) REVERT: E 409 GLN cc_start: 0.9411 (mm110) cc_final: 0.9079 (mp10) REVERT: E 442 ASP cc_start: 0.8984 (m-30) cc_final: 0.8028 (m-30) REVERT: E 444 LYS cc_start: 0.8223 (ptmm) cc_final: 0.6768 (mttt) REVERT: E 473 TYR cc_start: 0.8732 (t80) cc_final: 0.8335 (t80) REVERT: E 509 ARG cc_start: 0.8379 (mmt90) cc_final: 0.8014 (mmm-85) outliers start: 15 outliers final: 15 residues processed: 166 average time/residue: 0.0511 time to fit residues: 11.7064 Evaluate side-chains 165 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 330 ASN Chi-restraints excluded: chain A residue 491 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 A residue 588 PHE Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 361 CYS 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: 0.0010 chunk 27 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.0010 chunk 3 optimal weight: 2.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN E 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.120009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.101965 restraints weight = 28506.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.106280 restraints weight = 12959.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.109152 restraints weight = 7390.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.111090 restraints weight = 4764.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.112354 restraints weight = 3356.717| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4789 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= 0.150 Angle : 0.818 10.982 9067 Z= 0.402 Chirality : 0.046 0.294 962 Planarity : 0.005 0.055 1166 Dihedral : 5.556 37.004 968 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.33 % Allowed : 24.16 % Favored : 73.51 % 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: -0.76 (0.30), residues: 789 helix: 0.38 (0.26), residues: 407 sheet: -0.83 (0.73), residues: 59 loop : -1.56 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 403 TYR 0.025 0.002 TYR A 381 PHE 0.049 0.002 PHE A 452 TRP 0.041 0.002 TRP A 477 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6643) covalent geometry : angle 0.80736 ( 9038) SS BOND : bond 0.00605 ( 7) SS BOND : angle 2.57159 ( 14) hydrogen bonds : bond 0.04372 ( 322) hydrogen bonds : angle 5.04496 ( 916) link_NAG-ASN : bond 0.00251 ( 5) link_NAG-ASN : angle 2.39854 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1205.89 seconds wall clock time: 21 minutes 32.22 seconds (1292.22 seconds total)