Starting phenix.real_space_refine on Tue Feb 11 20:40:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fdg_31542/02_2025/7fdg_31542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdg_31542/02_2025/7fdg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7fdg_31542/02_2025/7fdg_31542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdg_31542/02_2025/7fdg_31542.map" model { file = "/net/cci-nas-00/data/ceres_data/7fdg_31542/02_2025/7fdg_31542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdg_31542/02_2025/7fdg_31542.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN: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: 6.91, per 1000 atoms: 1.07 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: 1.31 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.66 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: 1.80 Time building geometry restraints manager: 1.58 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: 1.930 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.730 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- 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 6643 Z= 0.422 Angle : 0.848 9.117 9038 Z= 0.487 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.002 TRP A 165 HIS 0.006 0.002 HIS A 535 PHE 0.020 0.002 PHE A 400 TYR 0.029 0.002 TYR E 380 ARG 0.006 0.001 ARG A 169 *********************** 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 : 0.631 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 29 LEU cc_start: 0.9484 (mt) cc_final: 0.9248 (mt) REVERT: A 76 GLN cc_start: 0.9324 (mm-40) cc_final: 0.8962 (mm-40) REVERT: A 97 LEU cc_start: 0.9367 (mt) cc_final: 0.9131 (mt) REVERT: A 127 TYR cc_start: 0.6916 (t80) cc_final: 0.6596 (t80) REVERT: A 224 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7900 (mt-10) REVERT: A 249 MET cc_start: 0.7900 (ttp) cc_final: 0.7628 (ttp) REVERT: A 258 PRO cc_start: 0.7916 (Cg_endo) cc_final: 0.7384 (Cg_exo) REVERT: A 362 THR cc_start: 0.8996 (m) cc_final: 0.8775 (m) REVERT: A 406 GLU cc_start: 0.8591 (tt0) cc_final: 0.8372 (tt0) REVERT: A 452 PHE cc_start: 0.9061 (t80) cc_final: 0.8802 (t80) REVERT: A 455 MET cc_start: 0.9132 (tmm) cc_final: 0.8475 (tmm) REVERT: A 481 LYS cc_start: 0.9130 (tppp) cc_final: 0.8662 (ttpt) REVERT: A 485 VAL cc_start: 0.8270 (t) cc_final: 0.7974 (t) REVERT: A 499 ASP cc_start: 0.8617 (m-30) cc_final: 0.8152 (t70) REVERT: A 503 LEU cc_start: 0.8573 (tp) cc_final: 0.8358 (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: 0.2012 time to fit residues: 50.3302 Evaluate side-chains 137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 7.9990 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 277 ASN A 338 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS A 552 GLN A 556 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.119076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.101465 restraints weight = 34440.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.105840 restraints weight = 13673.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.108672 restraints weight = 7324.676| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6643 Z= 0.222 Angle : 0.736 8.412 9038 Z= 0.376 Chirality : 0.047 0.227 962 Planarity : 0.005 0.051 1166 Dihedral : 7.450 56.793 968 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.60 % Allowed : 14.85 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.28), residues: 789 helix: 0.03 (0.25), residues: 379 sheet: -1.74 (0.62), residues: 62 loop : -1.68 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 477 HIS 0.005 0.001 HIS A 34 PHE 0.017 0.002 PHE A 588 TYR 0.027 0.002 TYR A 183 ARG 0.004 0.001 ARG A 219 *********************** 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 197 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9565 (mt) cc_final: 0.9309 (mt) REVERT: A 76 GLN cc_start: 0.9377 (mm-40) cc_final: 0.8646 (mm-40) REVERT: A 249 MET cc_start: 0.7955 (ttp) cc_final: 0.7744 (ttp) REVERT: A 258 PRO cc_start: 0.7800 (Cg_endo) cc_final: 0.7351 (Cg_exo) REVERT: A 275 TRP cc_start: 0.8778 (m-10) cc_final: 0.8495 (m-10) REVERT: A 323 MET cc_start: 0.7992 (mmm) cc_final: 0.6931 (mmm) REVERT: A 353 LYS cc_start: 0.9040 (mttt) cc_final: 0.7997 (ttmt) REVERT: A 360 MET cc_start: 0.7735 (tmm) cc_final: 0.7385 (tpt) REVERT: A 398 GLU cc_start: 0.8354 (pt0) cc_final: 0.8133 (pt0) REVERT: A 406 GLU cc_start: 0.8717 (tt0) cc_final: 0.8370 (tt0) REVERT: A 455 MET cc_start: 0.8998 (tmm) cc_final: 0.8664 (tmm) REVERT: A 477 TRP cc_start: 0.6819 (t-100) cc_final: 0.6247 (t-100) REVERT: A 481 LYS cc_start: 0.8891 (tppp) cc_final: 0.8484 (ttpt) REVERT: A 483 GLU cc_start: 0.9183 (tp30) cc_final: 0.8680 (mm-30) REVERT: A 487 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8078 (m) REVERT: E 357 ARG cc_start: 0.8576 (ttt180) cc_final: 0.7182 (mtt180) REVERT: E 442 ASP cc_start: 0.8981 (m-30) cc_final: 0.7882 (m-30) REVERT: E 444 LYS cc_start: 0.7835 (ptmm) cc_final: 0.7343 (ptpp) REVERT: E 455 LEU cc_start: 0.9275 (tp) cc_final: 0.9055 (tp) REVERT: E 509 ARG cc_start: 0.8494 (mtt180) cc_final: 0.7618 (mmm-85) outliers start: 9 outliers final: 4 residues processed: 194 average time/residue: 0.1758 time to fit residues: 45.3870 Evaluate side-chains 168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 322 ASN Chi-restraints excluded: chain A residue 487 VAL 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 24 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.118686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.099846 restraints weight = 40297.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.104514 restraints weight = 15285.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.107591 restraints weight = 8100.079| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6643 Z= 0.223 Angle : 0.723 9.773 9038 Z= 0.363 Chirality : 0.046 0.231 962 Planarity : 0.005 0.047 1166 Dihedral : 6.826 49.579 968 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.77 % Allowed : 17.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.29), residues: 789 helix: 0.48 (0.26), residues: 379 sheet: -1.67 (0.62), residues: 62 loop : -1.45 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 477 HIS 0.006 0.001 HIS A 265 PHE 0.025 0.002 PHE A 230 TYR 0.026 0.002 TYR A 183 ARG 0.004 0.000 ARG A 273 *********************** 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 192 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8836 (t80) cc_final: 0.8538 (t80) REVERT: A 82 MET cc_start: 0.9209 (mtm) cc_final: 0.8985 (mtm) REVERT: A 127 TYR cc_start: 0.6785 (t80) cc_final: 0.6183 (t80) REVERT: A 183 TYR cc_start: 0.9153 (t80) cc_final: 0.8376 (t80) REVERT: A 258 PRO cc_start: 0.7865 (Cg_endo) cc_final: 0.7435 (Cg_exo) REVERT: A 323 MET cc_start: 0.7960 (mmm) cc_final: 0.6816 (mmm) REVERT: A 353 LYS cc_start: 0.9028 (mttt) cc_final: 0.8007 (ttmt) REVERT: A 376 MET cc_start: 0.9267 (mmm) cc_final: 0.8963 (tpt) REVERT: A 398 GLU cc_start: 0.8408 (pt0) cc_final: 0.8164 (pt0) REVERT: A 406 GLU cc_start: 0.8870 (tt0) cc_final: 0.8499 (tt0) REVERT: A 452 PHE cc_start: 0.8686 (t80) cc_final: 0.8450 (t80) REVERT: A 481 LYS cc_start: 0.8894 (tppp) cc_final: 0.8489 (ttpt) REVERT: A 483 GLU cc_start: 0.9205 (tp30) cc_final: 0.8671 (mm-30) REVERT: A 499 ASP cc_start: 0.8441 (m-30) cc_final: 0.7920 (t0) REVERT: A 503 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8499 (mm) REVERT: A 565 PRO cc_start: 0.8738 (Cg_exo) cc_final: 0.8409 (Cg_endo) REVERT: A 567 THR cc_start: 0.9152 (m) cc_final: 0.8860 (p) REVERT: E 335 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7277 (mm) REVERT: E 357 ARG cc_start: 0.8483 (ttt180) cc_final: 0.7198 (mtt180) REVERT: E 396 TYR cc_start: 0.8561 (m-80) cc_final: 0.8163 (m-10) REVERT: E 398 ASP cc_start: 0.7929 (m-30) cc_final: 0.7671 (m-30) REVERT: E 421 TYR cc_start: 0.8731 (m-10) cc_final: 0.8527 (m-10) REVERT: E 423 TYR cc_start: 0.8678 (t80) cc_final: 0.7568 (t80) REVERT: E 444 LYS cc_start: 0.8035 (ptmm) cc_final: 0.6448 (mttt) REVERT: E 455 LEU cc_start: 0.9254 (tp) cc_final: 0.9019 (tp) REVERT: E 456 PHE cc_start: 0.8407 (m-80) cc_final: 0.7933 (m-80) REVERT: E 473 TYR cc_start: 0.8660 (t80) cc_final: 0.8163 (t80) REVERT: E 509 ARG cc_start: 0.8491 (mtt180) cc_final: 0.7852 (mmm-85) outliers start: 17 outliers final: 8 residues processed: 185 average time/residue: 0.1761 time to fit residues: 42.9292 Evaluate side-chains 169 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 271 TRP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 335 LEU 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 11 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 228 HIS A A 250 ASN A 330 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.113856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.095707 restraints weight = 35612.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.100120 restraints weight = 14678.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.102982 restraints weight = 8027.586| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6643 Z= 0.266 Angle : 0.733 11.152 9038 Z= 0.368 Chirality : 0.045 0.154 962 Planarity : 0.005 0.047 1166 Dihedral : 6.602 48.597 968 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.91 % Allowed : 19.65 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.29), residues: 789 helix: 0.55 (0.26), residues: 385 sheet: -1.54 (0.65), residues: 60 loop : -1.35 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 477 HIS 0.012 0.002 HIS A 265 PHE 0.026 0.002 PHE A 230 TYR 0.030 0.002 TYR A 381 ARG 0.003 0.001 ARG A 219 *********************** 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 185 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.736 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: 0.8857 (t80) cc_final: 0.8495 (t80) REVERT: A 75 GLU cc_start: 0.8563 (pp20) cc_final: 0.8006 (pp20) REVERT: A 76 GLN cc_start: 0.9326 (mm-40) cc_final: 0.8858 (mm-40) REVERT: A 258 PRO cc_start: 0.7616 (Cg_endo) cc_final: 0.7392 (Cg_exo) REVERT: A 323 MET cc_start: 0.7891 (mmm) cc_final: 0.6983 (mmm) REVERT: A 353 LYS cc_start: 0.8954 (mttt) cc_final: 0.7826 (ttmt) REVERT: A 383 MET cc_start: 0.8890 (tpt) cc_final: 0.8680 (tpt) REVERT: A 398 GLU cc_start: 0.8295 (pt0) cc_final: 0.8072 (pt0) REVERT: A 406 GLU cc_start: 0.8920 (tt0) cc_final: 0.8134 (tt0) REVERT: A 481 LYS cc_start: 0.8849 (tppp) cc_final: 0.8505 (ttpt) REVERT: A 483 GLU cc_start: 0.9226 (tp30) cc_final: 0.8703 (mm-30) REVERT: A 487 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7885 (m) REVERT: A 499 ASP cc_start: 0.8682 (m-30) cc_final: 0.7904 (t70) REVERT: A 565 PRO cc_start: 0.8823 (Cg_exo) cc_final: 0.8515 (Cg_endo) REVERT: A 567 THR cc_start: 0.9196 (m) cc_final: 0.8935 (p) REVERT: E 335 LEU cc_start: 0.7579 (mm) cc_final: 0.7302 (mm) REVERT: E 357 ARG cc_start: 0.8534 (ttt180) cc_final: 0.7262 (mtt180) REVERT: E 396 TYR cc_start: 0.8567 (m-80) cc_final: 0.8309 (m-10) REVERT: E 398 ASP cc_start: 0.7945 (m-30) cc_final: 0.7693 (m-30) REVERT: E 409 GLN cc_start: 0.9500 (mm110) cc_final: 0.9029 (mp10) REVERT: E 421 TYR cc_start: 0.8680 (m-10) cc_final: 0.8343 (m-10) REVERT: E 423 TYR cc_start: 0.8713 (t80) cc_final: 0.7596 (t80) REVERT: E 444 LYS cc_start: 0.7957 (ptmm) cc_final: 0.6454 (mttt) REVERT: E 455 LEU cc_start: 0.9270 (tp) cc_final: 0.9002 (tp) REVERT: E 456 PHE cc_start: 0.8489 (m-80) cc_final: 0.7790 (m-80) REVERT: E 509 ARG cc_start: 0.8493 (mtt180) cc_final: 0.7835 (mmm-85) outliers start: 19 outliers final: 13 residues processed: 177 average time/residue: 0.2064 time to fit residues: 47.9491 Evaluate side-chains 170 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 131 LYS 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 487 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 503 VAL 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 57 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN A 380 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 = 0.3867 r_free = 0.3867 target = 0.116324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.096971 restraints weight = 40901.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.101707 restraints weight = 15880.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104819 restraints weight = 8503.576| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6643 Z= 0.215 Angle : 0.703 8.890 9038 Z= 0.352 Chirality : 0.044 0.153 962 Planarity : 0.004 0.049 1166 Dihedral : 5.946 42.082 968 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.77 % Allowed : 20.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.30), residues: 789 helix: 0.69 (0.26), residues: 384 sheet: -1.37 (0.67), residues: 60 loop : -1.23 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 477 HIS 0.005 0.001 HIS A 241 PHE 0.025 0.001 PHE A 230 TYR 0.027 0.002 TYR A 381 ARG 0.002 0.000 ARG A 393 *********************** 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 188 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.668 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: 0.8823 (t80) cc_final: 0.8458 (t80) REVERT: A 75 GLU cc_start: 0.8610 (pp20) cc_final: 0.8055 (pp20) REVERT: A 76 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8852 (mm-40) REVERT: A 82 MET cc_start: 0.9038 (mtp) cc_final: 0.8779 (mtm) REVERT: A 258 PRO cc_start: 0.7479 (Cg_endo) cc_final: 0.7193 (Cg_exo) REVERT: A 323 MET cc_start: 0.7714 (mmm) cc_final: 0.6693 (mmm) REVERT: A 353 LYS cc_start: 0.8911 (mttt) cc_final: 0.7804 (ttmt) REVERT: A 392 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8733 (mm) REVERT: A 398 GLU cc_start: 0.8243 (pt0) cc_final: 0.7962 (pt0) REVERT: A 481 LYS cc_start: 0.8773 (tppp) cc_final: 0.8436 (ttpt) REVERT: A 483 GLU cc_start: 0.9225 (tp30) cc_final: 0.8710 (mm-30) REVERT: A 487 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.7961 (m) REVERT: A 499 ASP cc_start: 0.8687 (m-30) cc_final: 0.8044 (t70) REVERT: A 565 PRO cc_start: 0.8751 (Cg_exo) cc_final: 0.8419 (Cg_endo) REVERT: A 567 THR cc_start: 0.9196 (m) cc_final: 0.8905 (p) REVERT: E 357 ARG cc_start: 0.8469 (ttt180) cc_final: 0.7215 (mtt180) REVERT: E 409 GLN cc_start: 0.9502 (mm110) cc_final: 0.9076 (mp10) REVERT: E 421 TYR cc_start: 0.8675 (m-10) cc_final: 0.8327 (m-10) REVERT: E 442 ASP cc_start: 0.8984 (m-30) cc_final: 0.8102 (m-30) REVERT: E 444 LYS cc_start: 0.8010 (ptmm) cc_final: 0.6457 (mttt) REVERT: E 455 LEU cc_start: 0.9179 (tp) cc_final: 0.8954 (tp) REVERT: E 456 PHE cc_start: 0.8475 (m-80) cc_final: 0.7980 (m-80) REVERT: E 473 TYR cc_start: 0.8595 (t80) cc_final: 0.8072 (t80) REVERT: E 509 ARG cc_start: 0.8344 (mtt180) cc_final: 0.7768 (mmm-85) outliers start: 18 outliers final: 12 residues processed: 182 average time/residue: 0.1872 time to fit residues: 44.6014 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 : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 481 ASN 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 1 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.115543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098341 restraints weight = 27407.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.102346 restraints weight = 12658.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.104957 restraints weight = 7272.218| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6643 Z= 0.240 Angle : 0.722 10.617 9038 Z= 0.360 Chirality : 0.044 0.225 962 Planarity : 0.005 0.050 1166 Dihedral : 5.877 42.163 968 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.20 % Allowed : 20.67 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.30), residues: 789 helix: 0.75 (0.26), residues: 384 sheet: -1.37 (0.68), residues: 60 loop : -1.13 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 477 HIS 0.005 0.001 HIS A 241 PHE 0.024 0.002 PHE A 230 TYR 0.028 0.002 TYR A 381 ARG 0.003 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.769 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: 0.8867 (t80) cc_final: 0.8458 (t80) REVERT: A 75 GLU cc_start: 0.8605 (pp20) cc_final: 0.8018 (pp20) REVERT: A 76 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8834 (mm-40) REVERT: A 82 MET cc_start: 0.9043 (mtp) cc_final: 0.8800 (mtm) REVERT: A 206 ASP cc_start: 0.8130 (t0) cc_final: 0.7497 (t0) REVERT: A 258 PRO cc_start: 0.7523 (Cg_endo) cc_final: 0.7265 (Cg_exo) REVERT: A 323 MET cc_start: 0.7808 (mmm) cc_final: 0.6933 (mmm) REVERT: A 353 LYS cc_start: 0.8969 (mttt) cc_final: 0.7870 (ttmt) REVERT: A 376 MET cc_start: 0.8925 (tpt) cc_final: 0.8652 (tpp) REVERT: A 392 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8619 (mm) REVERT: A 481 LYS cc_start: 0.8816 (tppp) cc_final: 0.8512 (ttpt) REVERT: A 483 GLU cc_start: 0.9187 (tp30) cc_final: 0.8719 (mm-30) REVERT: A 487 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.7983 (m) REVERT: A 499 ASP cc_start: 0.8547 (m-30) cc_final: 0.7984 (t70) REVERT: A 565 PRO cc_start: 0.8839 (Cg_exo) cc_final: 0.8522 (Cg_endo) REVERT: A 567 THR cc_start: 0.9138 (m) cc_final: 0.8850 (p) REVERT: E 357 ARG cc_start: 0.8521 (ttt180) cc_final: 0.7214 (mtt180) REVERT: E 409 GLN cc_start: 0.9462 (mm110) cc_final: 0.9073 (mp10) REVERT: E 442 ASP cc_start: 0.9017 (m-30) cc_final: 0.8130 (m-30) REVERT: E 444 LYS cc_start: 0.8178 (ptmm) cc_final: 0.6667 (mttt) REVERT: E 456 PHE cc_start: 0.8452 (m-80) cc_final: 0.7801 (m-80) outliers start: 21 outliers final: 14 residues processed: 172 average time/residue: 0.2020 time to fit residues: 45.6102 Evaluate side-chains 171 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 360 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.117671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097412 restraints weight = 46890.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.102498 restraints weight = 17279.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.105824 restraints weight = 9041.656| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6643 Z= 0.210 Angle : 0.727 10.434 9038 Z= 0.358 Chirality : 0.044 0.203 962 Planarity : 0.005 0.052 1166 Dihedral : 5.628 39.656 968 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.35 % Allowed : 21.11 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.30), residues: 789 helix: 0.75 (0.26), residues: 384 sheet: -1.05 (0.68), residues: 59 loop : -1.11 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 168 HIS 0.006 0.001 HIS A 34 PHE 0.023 0.001 PHE A 230 TYR 0.028 0.002 TYR A 381 ARG 0.004 0.001 ARG A 273 *********************** 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 183 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.769 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: 0.8844 (t80) cc_final: 0.8474 (t80) REVERT: A 75 GLU cc_start: 0.8664 (pp20) cc_final: 0.8127 (pp20) REVERT: A 76 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8914 (mm-40) REVERT: A 82 MET cc_start: 0.9107 (mtp) cc_final: 0.8874 (mtm) REVERT: A 237 TYR cc_start: 0.9226 (t80) cc_final: 0.8693 (t80) REVERT: A 258 PRO cc_start: 0.7434 (Cg_endo) cc_final: 0.7160 (Cg_exo) REVERT: A 273 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6419 (ttt-90) REVERT: A 323 MET cc_start: 0.7799 (mmm) cc_final: 0.6930 (mmm) REVERT: A 353 LYS cc_start: 0.8922 (mttt) cc_final: 0.7842 (ttmt) REVERT: A 392 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8503 (mm) REVERT: A 398 GLU cc_start: 0.8412 (pt0) cc_final: 0.8019 (pt0) REVERT: A 430 GLU cc_start: 0.7634 (tp30) cc_final: 0.7394 (tp30) REVERT: A 461 TRP cc_start: 0.8147 (m-10) cc_final: 0.7789 (m-10) REVERT: A 481 LYS cc_start: 0.8799 (tppp) cc_final: 0.8514 (tppt) REVERT: A 483 GLU cc_start: 0.9206 (tp30) cc_final: 0.8742 (mm-30) REVERT: A 499 ASP cc_start: 0.8556 (m-30) cc_final: 0.8084 (t70) REVERT: A 565 PRO cc_start: 0.8756 (Cg_exo) cc_final: 0.8433 (Cg_endo) REVERT: A 567 THR cc_start: 0.9143 (m) cc_final: 0.8890 (p) REVERT: E 357 ARG cc_start: 0.8486 (ttt180) cc_final: 0.7207 (mtt180) REVERT: E 409 GLN cc_start: 0.9523 (mm110) cc_final: 0.9090 (mp10) REVERT: E 442 ASP cc_start: 0.8925 (m-30) cc_final: 0.7870 (m-30) REVERT: E 444 LYS cc_start: 0.8149 (ptmm) cc_final: 0.6632 (mttt) REVERT: E 473 TYR cc_start: 0.8618 (t80) cc_final: 0.8135 (t80) REVERT: E 509 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7704 (mmt90) outliers start: 22 outliers final: 14 residues processed: 177 average time/residue: 0.1985 time to fit residues: 46.4082 Evaluate side-chains 171 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 273 ARG Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 530 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 0.0020 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN A 330 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN E 422 ASN E 481 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.122474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.102872 restraints weight = 44882.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.107881 restraints weight = 16643.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.111105 restraints weight = 8703.038| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6643 Z= 0.211 Angle : 0.743 9.950 9038 Z= 0.368 Chirality : 0.045 0.170 962 Planarity : 0.005 0.054 1166 Dihedral : 5.493 38.656 968 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.20 % Allowed : 21.40 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.30), residues: 789 helix: 0.72 (0.27), residues: 392 sheet: -1.10 (0.68), residues: 59 loop : -1.24 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 168 HIS 0.004 0.001 HIS A 34 PHE 0.023 0.001 PHE A 230 TYR 0.026 0.002 TYR A 381 ARG 0.006 0.001 ARG E 403 *********************** 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 186 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8895 (t80) cc_final: 0.8451 (t80) REVERT: A 75 GLU cc_start: 0.8593 (pp20) cc_final: 0.8031 (pp20) REVERT: A 76 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8887 (mm-40) REVERT: A 82 MET cc_start: 0.9063 (mtp) cc_final: 0.8356 (ptm) REVERT: A 237 TYR cc_start: 0.9133 (t80) cc_final: 0.8671 (t80) REVERT: A 258 PRO cc_start: 0.7449 (Cg_endo) cc_final: 0.7192 (Cg_exo) REVERT: A 353 LYS cc_start: 0.9010 (mttt) cc_final: 0.7983 (ttmt) REVERT: A 383 MET cc_start: 0.8635 (tpt) cc_final: 0.8365 (tpt) REVERT: A 392 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8452 (mm) REVERT: A 398 GLU cc_start: 0.8335 (pt0) cc_final: 0.8059 (pt0) REVERT: A 406 GLU cc_start: 0.8842 (tt0) cc_final: 0.8229 (tt0) REVERT: A 461 TRP cc_start: 0.8099 (m-10) cc_final: 0.7764 (m-10) REVERT: A 481 LYS cc_start: 0.8819 (tppp) cc_final: 0.8469 (ttpt) REVERT: A 483 GLU cc_start: 0.9133 (tp30) cc_final: 0.8702 (mm-30) REVERT: A 487 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8046 (m) REVERT: A 499 ASP cc_start: 0.8439 (m-30) cc_final: 0.7617 (t0) REVERT: A 565 PRO cc_start: 0.8783 (Cg_exo) cc_final: 0.8486 (Cg_endo) REVERT: A 567 THR cc_start: 0.9033 (m) cc_final: 0.8760 (p) REVERT: E 354 ASN cc_start: 0.9117 (m-40) cc_final: 0.8899 (m110) REVERT: E 357 ARG cc_start: 0.8398 (ttt180) cc_final: 0.7143 (mtt180) REVERT: E 409 GLN cc_start: 0.9446 (mm110) cc_final: 0.9078 (mp10) REVERT: E 442 ASP cc_start: 0.8890 (m-30) cc_final: 0.7830 (m-30) REVERT: E 444 LYS cc_start: 0.8302 (ptmm) cc_final: 0.6736 (mttt) REVERT: E 473 TYR cc_start: 0.8713 (t80) cc_final: 0.8265 (t80) REVERT: E 509 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.7799 (mmt90) outliers start: 21 outliers final: 13 residues processed: 177 average time/residue: 0.1911 time to fit residues: 44.5406 Evaluate side-chains 171 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 325 GLN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 530 CYS 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 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN E 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.120529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.100520 restraints weight = 50491.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.105562 restraints weight = 18070.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.108894 restraints weight = 9391.280| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6643 Z= 0.241 Angle : 0.766 11.344 9038 Z= 0.374 Chirality : 0.046 0.182 962 Planarity : 0.005 0.052 1166 Dihedral : 5.502 38.241 968 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.30), residues: 789 helix: 0.72 (0.27), residues: 392 sheet: -1.10 (0.68), residues: 59 loop : -1.23 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 168 HIS 0.005 0.001 HIS A 34 PHE 0.022 0.002 PHE A 230 TYR 0.030 0.002 TYR A 127 ARG 0.005 0.001 ARG E 403 *********************** 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 170 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.696 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: 0.8899 (t80) cc_final: 0.8463 (t80) REVERT: A 75 GLU cc_start: 0.8575 (pp20) cc_final: 0.8013 (pp20) REVERT: A 76 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8872 (mm-40) REVERT: A 82 MET cc_start: 0.9084 (mtp) cc_final: 0.8878 (mtm) REVERT: A 237 TYR cc_start: 0.9113 (t80) cc_final: 0.8643 (t80) REVERT: A 258 PRO cc_start: 0.7484 (Cg_endo) cc_final: 0.7203 (Cg_exo) REVERT: A 323 MET cc_start: 0.7626 (mmm) cc_final: 0.6907 (mmm) REVERT: A 353 LYS cc_start: 0.9043 (mttt) cc_final: 0.8037 (ttmt) REVERT: A 376 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8657 (tpt) REVERT: A 392 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 406 GLU cc_start: 0.8872 (tt0) cc_final: 0.8289 (tt0) REVERT: A 430 GLU cc_start: 0.7702 (tp30) cc_final: 0.7084 (tp30) REVERT: A 435 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 474 MET cc_start: 0.7509 (mpp) cc_final: 0.7133 (mmm) REVERT: A 481 LYS cc_start: 0.8806 (tppp) cc_final: 0.8430 (tppt) REVERT: A 567 THR cc_start: 0.9047 (m) cc_final: 0.8772 (p) REVERT: E 357 ARG cc_start: 0.8367 (ttt180) cc_final: 0.7116 (mtt180) REVERT: E 409 GLN cc_start: 0.9440 (mm110) cc_final: 0.9107 (mp10) REVERT: E 442 ASP cc_start: 0.8919 (m-30) cc_final: 0.7901 (m-30) REVERT: E 444 LYS cc_start: 0.8336 (ptmm) cc_final: 0.6794 (mttt) REVERT: E 473 TYR cc_start: 0.8757 (t80) cc_final: 0.8296 (t80) REVERT: E 509 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.7892 (mmt90) outliers start: 17 outliers final: 14 residues processed: 164 average time/residue: 0.1929 time to fit residues: 42.1906 Evaluate side-chains 166 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 325 GLN Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 364 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS E 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.114535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.097204 restraints weight = 25244.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101094 restraints weight = 12110.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.103730 restraints weight = 7135.323| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6643 Z= 0.288 Angle : 0.782 11.519 9038 Z= 0.386 Chirality : 0.047 0.281 962 Planarity : 0.005 0.049 1166 Dihedral : 5.673 39.625 968 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.62 % Allowed : 23.58 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.31), residues: 789 helix: 0.74 (0.27), residues: 390 sheet: -1.61 (0.65), residues: 64 loop : -1.18 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 168 HIS 0.006 0.001 HIS A 378 PHE 0.048 0.002 PHE E 456 TYR 0.026 0.002 TYR A 381 ARG 0.004 0.001 ARG E 403 ********************** 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 164 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8862 (t80) cc_final: 0.8451 (t80) REVERT: A 75 GLU cc_start: 0.8631 (pp20) cc_final: 0.8052 (pp20) REVERT: A 76 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8895 (mm-40) REVERT: A 82 MET cc_start: 0.9130 (mtp) cc_final: 0.8863 (mtm) REVERT: A 237 TYR cc_start: 0.9225 (t80) cc_final: 0.8752 (t80) REVERT: A 258 PRO cc_start: 0.7566 (Cg_endo) cc_final: 0.7287 (Cg_exo) REVERT: A 323 MET cc_start: 0.7646 (mmm) cc_final: 0.7217 (mtt) REVERT: A 392 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8557 (mm) REVERT: A 408 MET cc_start: 0.9240 (ttm) cc_final: 0.9035 (ttm) REVERT: A 474 MET cc_start: 0.7597 (mpp) cc_final: 0.7172 (mmm) REVERT: A 481 LYS cc_start: 0.8797 (tppp) cc_final: 0.8451 (tppt) REVERT: A 567 THR cc_start: 0.9163 (m) cc_final: 0.8887 (p) REVERT: E 357 ARG cc_start: 0.8424 (ttt180) cc_final: 0.7229 (mtt180) REVERT: E 409 GLN cc_start: 0.9495 (mm110) cc_final: 0.9121 (mp10) REVERT: E 442 ASP cc_start: 0.8992 (m-30) cc_final: 0.8117 (m-30) REVERT: E 444 LYS cc_start: 0.8211 (ptmm) cc_final: 0.6715 (mttt) REVERT: E 501 TYR cc_start: 0.7705 (m-10) cc_final: 0.7469 (m-10) REVERT: E 507 PRO cc_start: 0.9333 (Cg_exo) cc_final: 0.9123 (Cg_endo) outliers start: 17 outliers final: 16 residues processed: 158 average time/residue: 0.1849 time to fit residues: 38.5362 Evaluate side-chains 162 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 376 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 491 VAL 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 364 ASP 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 56 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 76 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN E 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.123530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.104914 restraints weight = 36958.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.109536 restraints weight = 15426.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.112623 restraints weight = 8407.450| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6643 Z= 0.210 Angle : 0.790 11.152 9038 Z= 0.383 Chirality : 0.045 0.194 962 Planarity : 0.005 0.051 1166 Dihedral : 5.391 37.233 968 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.62 % Allowed : 23.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.30), residues: 789 helix: 0.71 (0.27), residues: 398 sheet: -1.12 (0.69), residues: 59 loop : -1.22 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 168 HIS 0.006 0.001 HIS A 34 PHE 0.024 0.002 PHE A 230 TYR 0.028 0.002 TYR A 183 ARG 0.005 0.001 ARG E 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2511.49 seconds wall clock time: 45 minutes 42.74 seconds (2742.74 seconds total)