Starting phenix.real_space_refine on Tue Mar 11 20:11:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fdg_31542/03_2025/7fdg_31542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdg_31542/03_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_31542/03_2025/7fdg_31542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdg_31542/03_2025/7fdg_31542.map" model { file = "/net/cci-nas-00/data/ceres_data/7fdg_31542/03_2025/7fdg_31542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdg_31542/03_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-5624/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: 7.63, per 1000 atoms: 1.18 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: 1.81 Conformation dependent library (CDL) restraints added in 1.7 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: 0.67 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: 1.77 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2068 1.35 - 1.47: 1800 1.47 - 1.60: 2721 1.60 - 1.72: 0 1.72 - 1.85: 54 Bond restraints: 6643 Sorted by residual: bond pdb=" C GLY A 319 " pdb=" N LEU A 320 " ideal model delta sigma weight residual 1.329 1.279 0.050 1.86e-02 2.89e+03 7.16e+00 bond pdb=" C VAL A 283 " pdb=" N PRO A 284 " ideal model delta sigma weight residual 1.336 1.308 0.028 1.23e-02 6.61e+03 5.19e+00 bond pdb=" C TYR E 495 " pdb=" N GLY E 496 " ideal model delta sigma weight residual 1.332 1.323 0.009 5.00e-03 4.00e+04 3.39e+00 bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.66e+00 bond pdb=" CA CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sigma weight residual 1.530 1.508 0.022 1.53e-02 4.27e+03 2.13e+00 ... (remaining 6638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 8632 1.82 - 3.65: 351 3.65 - 5.47: 41 5.47 - 7.29: 10 7.29 - 9.12: 4 Bond angle restraints: 9038 Sorted by residual: angle pdb=" C PHE E 464 " pdb=" N GLU E 465 " pdb=" CA GLU E 465 " ideal model delta sigma weight residual 122.93 115.46 7.47 1.45e+00 4.76e-01 2.66e+01 angle pdb=" CA CYS E 379 " pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " ideal model delta sigma weight residual 114.40 123.52 -9.12 2.30e+00 1.89e-01 1.57e+01 angle pdb=" N CYS E 379 " pdb=" CA CYS E 379 " pdb=" C CYS E 379 " ideal model delta sigma weight residual 107.88 113.28 -5.40 1.41e+00 5.03e-01 1.47e+01 angle pdb=" CA PHE E 464 " pdb=" C PHE E 464 " pdb=" N GLU E 465 " ideal model delta sigma weight residual 116.21 120.46 -4.25 1.29e+00 6.01e-01 1.09e+01 angle pdb=" C GLN E 409 " pdb=" N ILE E 410 " pdb=" CA ILE E 410 " ideal model delta sigma weight residual 122.59 118.97 3.62 1.10e+00 8.26e-01 1.08e+01 ... (remaining 9033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3501 17.31 - 34.63: 354 34.63 - 51.94: 81 51.94 - 69.26: 29 69.26 - 86.57: 13 Dihedral angle restraints: 3978 sinusoidal: 1649 harmonic: 2329 Sorted by residual: dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 10.31 82.69 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CA VAL E 524 " pdb=" C VAL E 524 " pdb=" N CYS E 525 " pdb=" CA CYS E 525 " ideal model delta harmonic sigma weight residual 180.00 143.31 36.69 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 30.17 62.83 1 1.00e+01 1.00e-02 5.22e+01 ... (remaining 3975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 542 0.035 - 0.071: 290 0.071 - 0.106: 107 0.106 - 0.142: 20 0.142 - 0.177: 3 Chirality restraints: 962 Sorted by residual: chirality pdb=" CA CYS E 379 " pdb=" N CYS E 379 " pdb=" C CYS E 379 " pdb=" CB CYS E 379 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CB ILE E 410 " pdb=" CA ILE E 410 " pdb=" CG1 ILE E 410 " pdb=" CG2 ILE E 410 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 959 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A 500 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 283 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 284 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 473 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C TRP A 473 " -0.030 2.00e-02 2.50e+03 pdb=" O TRP A 473 " 0.011 2.00e-02 2.50e+03 pdb=" N MET A 474 " 0.010 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 170 2.63 - 3.20: 6699 3.20 - 3.76: 10796 3.76 - 4.33: 14302 4.33 - 4.90: 21797 Nonbonded interactions: 53764 Sorted by model distance: nonbonded pdb=" O THR A 118 " pdb=" OG1 THR A 122 " model vdw 2.061 3.040 nonbonded pdb=" O ASN A 103 " pdb=" OG SER A 106 " model vdw 2.093 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR E 500 " model vdw 2.138 3.040 nonbonded pdb=" O HIS A 417 " pdb=" OG SER A 420 " model vdw 2.142 3.040 nonbonded pdb=" O THR A 449 " pdb=" OG1 THR A 453 " model vdw 2.157 3.040 ... (remaining 53759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 23.920 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.900 ------------------------------------------------------------------------------- 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 : 0.820 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: 0.2009 time to fit residues: 50.4800 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 = 0.101466 restraints weight = 34440.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.105811 restraints weight = 13674.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.108654 restraints weight = 7339.445| |-----------------------------------------------------------------------------| 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: 0.7656 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 : 0.706 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: 0.9564 (mt) cc_final: 0.9308 (mt) REVERT: A 76 GLN cc_start: 0.9378 (mm-40) cc_final: 0.8648 (mm-40) REVERT: A 249 MET cc_start: 0.7953 (ttp) cc_final: 0.7742 (ttp) REVERT: A 258 PRO cc_start: 0.7801 (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: 0.7989 (mmm) cc_final: 0.6927 (mmm) REVERT: A 353 LYS cc_start: 0.9040 (mttt) cc_final: 0.7997 (ttmt) REVERT: A 360 MET cc_start: 0.7737 (tmm) cc_final: 0.7385 (tpt) REVERT: A 398 GLU cc_start: 0.8350 (pt0) cc_final: 0.8129 (pt0) REVERT: A 406 GLU cc_start: 0.8718 (tt0) cc_final: 0.8370 (tt0) REVERT: A 455 MET cc_start: 0.8998 (tmm) cc_final: 0.8668 (tmm) REVERT: A 477 TRP cc_start: 0.6818 (t-100) cc_final: 0.6243 (t-100) REVERT: A 481 LYS cc_start: 0.8889 (tppp) cc_final: 0.8483 (ttpt) REVERT: A 483 GLU cc_start: 0.9186 (tp30) cc_final: 0.8682 (mm-30) REVERT: A 487 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.8074 (m) REVERT: E 357 ARG cc_start: 0.8577 (ttt180) cc_final: 0.7184 (mtt180) REVERT: E 442 ASP cc_start: 0.8981 (m-30) cc_final: 0.7881 (m-30) REVERT: E 444 LYS cc_start: 0.7836 (ptmm) cc_final: 0.7345 (ptpp) REVERT: E 455 LEU cc_start: 0.9275 (tp) cc_final: 0.9056 (tp) REVERT: E 509 ARG cc_start: 0.8496 (mtt180) cc_final: 0.7620 (mmm-85) outliers start: 9 outliers final: 4 residues processed: 194 average time/residue: 0.1805 time to fit residues: 47.2295 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 : 0.782 ------------------------------------------------------------------------------- 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: 9.9990 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.117162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099091 restraints weight = 40499.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.103629 restraints weight = 15367.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.106633 restraints weight = 8089.411| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6643 Z= 0.253 Angle : 0.733 9.225 9038 Z= 0.370 Chirality : 0.047 0.236 962 Planarity : 0.005 0.046 1166 Dihedral : 7.010 51.688 968 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.20 % Allowed : 16.45 % Favored : 80.35 % 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: -0.89 (0.29), residues: 789 helix: 0.42 (0.25), residues: 379 sheet: -1.68 (0.63), residues: 62 loop : -1.48 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 477 HIS 0.006 0.001 HIS A 265 PHE 0.026 0.002 PHE A 230 TYR 0.028 0.002 TYR A 183 ARG 0.004 0.001 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 193 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.698 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: 0.8868 (t80) cc_final: 0.8614 (t80) REVERT: A 76 GLN cc_start: 0.9334 (mm-40) cc_final: 0.8752 (mm-40) REVERT: A 82 MET cc_start: 0.9184 (mtm) cc_final: 0.8961 (mtm) REVERT: A 127 TYR cc_start: 0.6782 (t80) cc_final: 0.6192 (t80) REVERT: A 183 TYR cc_start: 0.9131 (t80) cc_final: 0.8483 (t80) REVERT: A 249 MET cc_start: 0.7980 (ttp) cc_final: 0.7711 (ttp) REVERT: A 258 PRO cc_start: 0.7925 (Cg_endo) cc_final: 0.7488 (Cg_exo) REVERT: A 323 MET cc_start: 0.8015 (mmm) cc_final: 0.6896 (mmm) REVERT: A 353 LYS cc_start: 0.9063 (mttt) cc_final: 0.8059 (ttmt) REVERT: A 376 MET cc_start: 0.9258 (mmm) cc_final: 0.8955 (tpt) REVERT: A 398 GLU cc_start: 0.8440 (pt0) cc_final: 0.8190 (pt0) REVERT: A 406 GLU cc_start: 0.8873 (tt0) cc_final: 0.8498 (tt0) REVERT: A 481 LYS cc_start: 0.8911 (tppp) cc_final: 0.8532 (ttpt) REVERT: A 483 GLU cc_start: 0.9184 (tp30) cc_final: 0.8680 (mm-30) REVERT: A 487 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8012 (m) REVERT: A 499 ASP cc_start: 0.8485 (m-30) cc_final: 0.7971 (t70) REVERT: A 503 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 565 PRO cc_start: 0.8832 (Cg_exo) cc_final: 0.8498 (Cg_endo) REVERT: A 567 THR cc_start: 0.9100 (m) cc_final: 0.8759 (p) REVERT: E 335 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7282 (mm) REVERT: E 357 ARG cc_start: 0.8514 (ttt180) cc_final: 0.7261 (mtt180) REVERT: E 398 ASP cc_start: 0.7945 (m-30) cc_final: 0.7689 (m-30) REVERT: E 421 TYR cc_start: 0.8723 (m-10) cc_final: 0.8515 (m-10) REVERT: E 423 TYR cc_start: 0.8678 (t80) cc_final: 0.7660 (t80) REVERT: E 444 LYS cc_start: 0.8054 (ptmm) cc_final: 0.6469 (mttt) REVERT: E 455 LEU cc_start: 0.9288 (tp) cc_final: 0.9030 (tp) REVERT: E 456 PHE cc_start: 0.8436 (m-80) cc_final: 0.7979 (m-80) REVERT: E 473 TYR cc_start: 0.8674 (t80) cc_final: 0.8153 (t80) outliers start: 20 outliers final: 10 residues processed: 184 average time/residue: 0.1786 time to fit residues: 44.0589 Evaluate side-chains 169 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 487 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain 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 503 VAL 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: 9.9990 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.121112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.102065 restraints weight = 34616.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.106577 restraints weight = 14282.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.109591 restraints weight = 7811.821| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6643 Z= 0.226 Angle : 0.715 9.303 9038 Z= 0.358 Chirality : 0.044 0.147 962 Planarity : 0.005 0.048 1166 Dihedral : 6.504 47.853 968 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.62 % Allowed : 18.49 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.29), residues: 789 helix: 0.60 (0.26), residues: 385 sheet: -1.53 (0.65), residues: 60 loop : -1.35 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 477 HIS 0.005 0.001 HIS A 241 PHE 0.025 0.002 PHE A 230 TYR 0.029 0.002 TYR A 381 ARG 0.003 0.000 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: 17 poor density : 168 time to evaluate : 0.707 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: 0.8881 (t80) cc_final: 0.8505 (t80) REVERT: A 75 GLU cc_start: 0.8543 (pp20) cc_final: 0.7972 (pp20) REVERT: A 76 GLN cc_start: 0.9302 (mm-40) cc_final: 0.8839 (mm-40) REVERT: A 249 MET cc_start: 0.8032 (ttp) cc_final: 0.7823 (ttp) REVERT: A 258 PRO cc_start: 0.7827 (Cg_endo) cc_final: 0.7419 (Cg_exo) REVERT: A 323 MET cc_start: 0.7808 (mmm) cc_final: 0.6924 (mmm) REVERT: A 353 LYS cc_start: 0.8966 (mttt) cc_final: 0.7945 (ttmt) REVERT: A 383 MET cc_start: 0.8794 (tpt) cc_final: 0.8582 (tpt) REVERT: A 398 GLU cc_start: 0.8264 (pt0) cc_final: 0.8058 (pt0) REVERT: A 406 GLU cc_start: 0.8844 (tt0) cc_final: 0.8000 (tt0) REVERT: A 481 LYS cc_start: 0.8886 (tppp) cc_final: 0.8487 (ttpt) REVERT: A 483 GLU cc_start: 0.9196 (tp30) cc_final: 0.8668 (mm-30) REVERT: A 487 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8121 (m) REVERT: A 499 ASP cc_start: 0.8527 (m-30) cc_final: 0.7887 (t0) REVERT: A 565 PRO cc_start: 0.8777 (Cg_exo) cc_final: 0.8470 (Cg_endo) REVERT: A 567 THR cc_start: 0.9131 (m) cc_final: 0.8876 (p) REVERT: E 335 LEU cc_start: 0.7590 (mm) cc_final: 0.7316 (mm) REVERT: E 357 ARG cc_start: 0.8453 (ttt180) cc_final: 0.7189 (mtt180) REVERT: E 398 ASP cc_start: 0.7927 (m-30) cc_final: 0.7686 (m-30) REVERT: E 409 GLN cc_start: 0.9450 (mm110) cc_final: 0.9056 (mp10) REVERT: E 421 TYR cc_start: 0.8696 (m-10) cc_final: 0.8400 (m-10) REVERT: E 423 TYR cc_start: 0.8735 (t80) cc_final: 0.7658 (t80) REVERT: E 444 LYS cc_start: 0.8065 (ptmm) cc_final: 0.6492 (mttt) REVERT: E 455 LEU cc_start: 0.9265 (tp) cc_final: 0.9017 (tp) REVERT: E 456 PHE cc_start: 0.8460 (m-80) cc_final: 0.7999 (m-80) REVERT: E 473 TYR cc_start: 0.8623 (t80) cc_final: 0.8100 (t80) REVERT: E 509 ARG cc_start: 0.8442 (mtt180) cc_final: 0.7843 (mmm-85) outliers start: 17 outliers final: 12 residues processed: 179 average time/residue: 0.1853 time to fit residues: 43.6209 Evaluate side-chains 167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 241 HIS 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 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.0570 chunk 38 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS A 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.124403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.104421 restraints weight = 39622.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.109195 restraints weight = 15725.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.112400 restraints weight = 8491.387| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6643 Z= 0.202 Angle : 0.707 8.967 9038 Z= 0.354 Chirality : 0.043 0.154 962 Planarity : 0.005 0.051 1166 Dihedral : 5.791 40.022 968 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.77 % Allowed : 20.09 % Favored : 77.15 % 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: -0.47 (0.30), residues: 789 helix: 0.72 (0.26), residues: 387 sheet: -1.45 (0.66), residues: 60 loop : -1.27 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.026 0.001 PHE A 230 TYR 0.028 0.002 TYR A 381 ARG 0.007 0.000 ARG E 403 *********************** 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 182 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.753 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: 0.8868 (t80) cc_final: 0.8477 (t80) REVERT: A 75 GLU cc_start: 0.8532 (pp20) cc_final: 0.7986 (pp20) REVERT: A 76 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8886 (mm-40) REVERT: A 249 MET cc_start: 0.8061 (ttp) cc_final: 0.7823 (ttp) REVERT: A 258 PRO cc_start: 0.7536 (Cg_endo) cc_final: 0.7045 (Cg_exo) REVERT: A 323 MET cc_start: 0.7569 (mmm) cc_final: 0.6771 (mmm) REVERT: A 353 LYS cc_start: 0.8936 (mttt) cc_final: 0.7948 (ttmt) REVERT: A 376 MET cc_start: 0.8820 (tpt) cc_final: 0.8477 (tpp) REVERT: A 392 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8725 (mm) REVERT: A 398 GLU cc_start: 0.8220 (pt0) cc_final: 0.7962 (pt0) REVERT: A 461 TRP cc_start: 0.8207 (m-10) cc_final: 0.7835 (m-10) REVERT: A 481 LYS cc_start: 0.8870 (tppp) cc_final: 0.8514 (ttpt) REVERT: A 483 GLU cc_start: 0.9170 (tp30) cc_final: 0.8697 (mm-30) REVERT: A 499 ASP cc_start: 0.8633 (m-30) cc_final: 0.8056 (t70) REVERT: A 505 HIS cc_start: 0.8515 (m-70) cc_final: 0.8285 (m-70) REVERT: A 565 PRO cc_start: 0.8768 (Cg_exo) cc_final: 0.8457 (Cg_endo) REVERT: A 567 THR cc_start: 0.9092 (m) cc_final: 0.8802 (p) REVERT: E 357 ARG cc_start: 0.8463 (ttt180) cc_final: 0.7148 (mtt180) REVERT: E 409 GLN cc_start: 0.9429 (mm110) cc_final: 0.9117 (mp10) REVERT: E 442 ASP cc_start: 0.8988 (m-30) cc_final: 0.8253 (m-30) REVERT: E 444 LYS cc_start: 0.8178 (ptmm) cc_final: 0.6603 (mttt) REVERT: E 456 PHE cc_start: 0.8408 (m-80) cc_final: 0.7998 (m-80) REVERT: E 473 TYR cc_start: 0.8554 (t80) cc_final: 0.8037 (t80) REVERT: E 509 ARG cc_start: 0.8319 (mtt180) cc_final: 0.8065 (mmm-85) outliers start: 18 outliers final: 13 residues processed: 177 average time/residue: 0.1845 time to fit residues: 43.2117 Evaluate side-chains 172 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** 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 ** 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 = 0.4024 r_free = 0.4024 target = 0.124643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.106307 restraints weight = 26484.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.110468 restraints weight = 12353.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.113282 restraints weight = 7163.307| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6643 Z= 0.206 Angle : 0.711 9.476 9038 Z= 0.352 Chirality : 0.044 0.235 962 Planarity : 0.005 0.051 1166 Dihedral : 5.585 39.042 968 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.77 % Allowed : 20.82 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.30), residues: 789 helix: 0.79 (0.26), residues: 391 sheet: -1.46 (0.65), residues: 60 loop : -1.15 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 477 HIS 0.005 0.001 HIS A 505 PHE 0.022 0.001 PHE A 230 TYR 0.028 0.002 TYR A 381 ARG 0.005 0.001 ARG E 403 *********************** 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: 18 poor density : 159 time to evaluate : 0.790 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: 0.8882 (t80) cc_final: 0.8482 (t80) REVERT: A 75 GLU cc_start: 0.8583 (pp20) cc_final: 0.8040 (pp20) REVERT: A 76 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8885 (mm-40) REVERT: A 258 PRO cc_start: 0.7649 (Cg_endo) cc_final: 0.7158 (Cg_exo) REVERT: A 323 MET cc_start: 0.7706 (mmm) cc_final: 0.6833 (mmm) REVERT: A 353 LYS cc_start: 0.8930 (mttt) cc_final: 0.7951 (ttmt) REVERT: A 376 MET cc_start: 0.8813 (tpt) cc_final: 0.8531 (tpp) REVERT: A 392 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8553 (mm) REVERT: A 398 GLU cc_start: 0.8243 (pt0) cc_final: 0.7973 (pt0) REVERT: A 406 GLU cc_start: 0.8730 (tt0) cc_final: 0.8322 (tt0) REVERT: A 430 GLU cc_start: 0.7674 (tp30) cc_final: 0.7423 (tp30) REVERT: A 481 LYS cc_start: 0.8888 (tppp) cc_final: 0.8544 (ttpt) REVERT: A 483 GLU cc_start: 0.9147 (tp30) cc_final: 0.8693 (mm-30) REVERT: A 499 ASP cc_start: 0.8636 (m-30) cc_final: 0.8060 (t0) REVERT: A 565 PRO cc_start: 0.8694 (Cg_exo) cc_final: 0.8388 (Cg_endo) REVERT: E 357 ARG cc_start: 0.8381 (ttt180) cc_final: 0.7051 (mtt180) REVERT: E 409 GLN cc_start: 0.9387 (mm110) cc_final: 0.9123 (mp10) REVERT: E 442 ASP cc_start: 0.8989 (m-30) cc_final: 0.8237 (m-30) REVERT: E 444 LYS cc_start: 0.8214 (ptmm) cc_final: 0.6642 (mttt) REVERT: E 473 TYR cc_start: 0.8572 (t80) cc_final: 0.8110 (t80) outliers start: 18 outliers final: 13 residues processed: 173 average time/residue: 0.1997 time to fit residues: 46.4038 Evaluate side-chains 165 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 530 CYS Chi-restraints excluded: chain A residue 579 MET 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: 1.9990 chunk 24 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 0.0010 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.116170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096438 restraints weight = 47217.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.101471 restraints weight = 17536.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104726 restraints weight = 9190.216| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4109 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= 0.262 Angle : 0.738 10.479 9038 Z= 0.370 Chirality : 0.046 0.218 962 Planarity : 0.005 0.050 1166 Dihedral : 5.716 40.465 968 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.77 % Allowed : 21.11 % 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: -0.41 (0.30), residues: 789 helix: 0.77 (0.26), residues: 389 sheet: -1.55 (0.65), residues: 64 loop : -1.20 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 168 HIS 0.005 0.001 HIS A 378 PHE 0.039 0.002 PHE E 456 TYR 0.028 0.002 TYR A 381 ARG 0.004 0.001 ARG E 403 *********************** 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 168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8882 (t80) cc_final: 0.8475 (t80) REVERT: A 75 GLU cc_start: 0.8633 (pp20) cc_final: 0.8088 (pp20) REVERT: A 76 GLN cc_start: 0.9295 (mm-40) cc_final: 0.8896 (mm-40) REVERT: A 206 ASP cc_start: 0.8151 (t0) cc_final: 0.7585 (t0) REVERT: A 258 PRO cc_start: 0.7473 (Cg_endo) cc_final: 0.7191 (Cg_exo) REVERT: A 323 MET cc_start: 0.7882 (mmm) cc_final: 0.6772 (mtt) REVERT: A 392 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8559 (mm) REVERT: A 406 GLU cc_start: 0.8923 (tt0) cc_final: 0.8534 (tt0) REVERT: A 481 LYS cc_start: 0.8870 (tppp) cc_final: 0.8541 (tppt) REVERT: A 483 GLU cc_start: 0.9178 (tp30) cc_final: 0.8679 (mm-30) REVERT: A 498 CYS cc_start: 0.7781 (t) cc_final: 0.6437 (t) REVERT: A 499 ASP cc_start: 0.8543 (m-30) cc_final: 0.7539 (t0) REVERT: E 357 ARG cc_start: 0.8483 (ttt180) cc_final: 0.7201 (mtt180) REVERT: E 409 GLN cc_start: 0.9500 (mm110) cc_final: 0.9132 (mp10) REVERT: E 442 ASP cc_start: 0.8925 (m-30) cc_final: 0.8235 (m-30) REVERT: E 444 LYS cc_start: 0.8254 (ptmm) cc_final: 0.6748 (mttt) REVERT: E 495 TYR cc_start: 0.8460 (m-80) cc_final: 0.8168 (m-80) REVERT: E 501 TYR cc_start: 0.7641 (m-10) cc_final: 0.7426 (m-10) outliers start: 18 outliers final: 12 residues processed: 162 average time/residue: 0.1795 time to fit residues: 38.6984 Evaluate side-chains 161 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 392 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 588 PHE Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS 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 = 0.3857 r_free = 0.3857 target = 0.115473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.095362 restraints weight = 46372.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.100352 restraints weight = 17600.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.103695 restraints weight = 9288.975| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4283 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= 0.258 Angle : 0.742 9.963 9038 Z= 0.374 Chirality : 0.045 0.172 962 Planarity : 0.005 0.051 1166 Dihedral : 5.741 40.845 968 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % 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: -0.46 (0.30), residues: 789 helix: 0.72 (0.26), residues: 391 sheet: -1.61 (0.65), residues: 64 loop : -1.22 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 168 HIS 0.006 0.001 HIS A 540 PHE 0.026 0.002 PHE A 274 TYR 0.034 0.002 TYR A 237 ARG 0.004 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 172 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.776 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: 0.8880 (t80) cc_final: 0.8478 (t80) REVERT: A 75 GLU cc_start: 0.8646 (pp20) cc_final: 0.8115 (pp20) REVERT: A 76 GLN cc_start: 0.9300 (mm-40) cc_final: 0.8917 (mm-40) REVERT: A 258 PRO cc_start: 0.7488 (Cg_endo) cc_final: 0.7203 (Cg_exo) REVERT: A 323 MET cc_start: 0.7914 (mmm) cc_final: 0.6975 (mmm) REVERT: A 353 LYS cc_start: 0.9035 (tttt) cc_final: 0.7849 (ttmt) REVERT: A 392 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8556 (mm) REVERT: A 398 GLU cc_start: 0.8367 (pt0) cc_final: 0.8029 (pt0) REVERT: A 461 TRP cc_start: 0.8277 (m-10) cc_final: 0.7995 (m-10) REVERT: A 481 LYS cc_start: 0.8851 (tppp) cc_final: 0.8512 (ttpt) REVERT: A 483 GLU cc_start: 0.9217 (tp30) cc_final: 0.8701 (mm-30) REVERT: A 487 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.7944 (m) REVERT: A 498 CYS cc_start: 0.8015 (t) cc_final: 0.7711 (t) REVERT: A 567 THR cc_start: 0.9169 (m) cc_final: 0.8885 (p) REVERT: E 357 ARG cc_start: 0.8500 (ttt180) cc_final: 0.7217 (mtt180) REVERT: E 409 GLN cc_start: 0.9524 (mm110) cc_final: 0.9133 (mp10) REVERT: E 442 ASP cc_start: 0.8935 (m-30) cc_final: 0.7927 (m-30) REVERT: E 444 LYS cc_start: 0.8209 (ptmm) cc_final: 0.6748 (mttt) REVERT: E 495 TYR cc_start: 0.8512 (m-80) cc_final: 0.8195 (m-80) REVERT: E 509 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7980 (mmt-90) outliers start: 21 outliers final: 15 residues processed: 161 average time/residue: 0.1909 time to fit residues: 40.3692 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 : 0.766 ------------------------------------------------------------------------------- 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 277 ASN 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 513 ILE 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: 3.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.116869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.096100 restraints weight = 51341.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.101324 restraints weight = 18554.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.104790 restraints weight = 9669.617| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6643 Z= 0.249 Angle : 0.759 11.835 9038 Z= 0.376 Chirality : 0.046 0.196 962 Planarity : 0.005 0.052 1166 Dihedral : 5.712 41.688 968 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.62 % Allowed : 21.98 % 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: -0.50 (0.30), residues: 789 helix: 0.67 (0.26), residues: 391 sheet: -1.62 (0.64), residues: 64 loop : -1.23 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 168 HIS 0.008 0.001 HIS A 540 PHE 0.029 0.002 PHE A 274 TYR 0.044 0.002 TYR A 237 ARG 0.003 0.001 ARG A 219 *********************** 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 166 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.745 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: 0.8886 (t80) cc_final: 0.8473 (t80) REVERT: A 75 GLU cc_start: 0.8651 (pp20) cc_final: 0.8034 (pp20) REVERT: A 76 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8858 (mm-40) REVERT: A 258 PRO cc_start: 0.7499 (Cg_endo) cc_final: 0.7229 (Cg_exo) REVERT: A 323 MET cc_start: 0.7991 (mmm) cc_final: 0.7145 (mmm) REVERT: A 353 LYS cc_start: 0.9050 (tttt) cc_final: 0.7890 (ttmt) REVERT: A 392 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8515 (mm) REVERT: A 398 GLU cc_start: 0.8375 (pt0) cc_final: 0.8113 (pt0) REVERT: A 481 LYS cc_start: 0.8849 (tppp) cc_final: 0.8499 (ttpt) REVERT: A 483 GLU cc_start: 0.9204 (tp30) cc_final: 0.8680 (mm-30) REVERT: A 487 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.7958 (m) REVERT: A 567 THR cc_start: 0.9172 (m) cc_final: 0.8920 (p) REVERT: E 357 ARG cc_start: 0.8442 (ttt180) cc_final: 0.7192 (mtt180) REVERT: E 409 GLN cc_start: 0.9508 (mm110) cc_final: 0.9170 (mp10) REVERT: E 442 ASP cc_start: 0.8908 (m-30) cc_final: 0.7818 (m-30) REVERT: E 444 LYS cc_start: 0.8223 (ptmm) cc_final: 0.6757 (mttt) REVERT: E 473 TYR cc_start: 0.8782 (t80) cc_final: 0.8333 (t80) REVERT: E 507 PRO cc_start: 0.9266 (Cg_exo) cc_final: 0.9011 (Cg_endo) REVERT: E 509 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.7975 (mmt-90) outliers start: 17 outliers final: 15 residues processed: 159 average time/residue: 0.1864 time to fit residues: 39.2794 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 : 0.746 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP 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 513 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 588 PHE Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3970 r_free = 0.3970 target = 0.120300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.103039 restraints weight = 25591.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.107060 restraints weight = 12166.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.109727 restraints weight = 7070.629| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6643 Z= 0.227 Angle : 0.759 12.112 9038 Z= 0.374 Chirality : 0.045 0.156 962 Planarity : 0.005 0.052 1166 Dihedral : 5.576 39.725 968 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.47 % Allowed : 22.56 % Favored : 74.96 % 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: -0.44 (0.30), residues: 789 helix: 0.66 (0.26), residues: 391 sheet: -1.24 (0.69), residues: 53 loop : -1.21 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A 168 HIS 0.008 0.001 HIS A 540 PHE 0.028 0.002 PHE A 274 TYR 0.037 0.002 TYR A 237 ARG 0.005 0.001 ARG A 177 ********************** 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 170 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.9243 (ttp) cc_final: 0.8314 (ttt) REVERT: A 72 PHE cc_start: 0.8899 (t80) cc_final: 0.8509 (t80) REVERT: A 75 GLU cc_start: 0.8574 (pp20) cc_final: 0.8048 (pp20) REVERT: A 76 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8954 (mm-40) REVERT: A 171 GLU cc_start: 0.8126 (tp30) cc_final: 0.7575 (tt0) REVERT: A 258 PRO cc_start: 0.7522 (Cg_endo) cc_final: 0.7232 (Cg_exo) REVERT: A 297 MET cc_start: 0.8270 (tpp) cc_final: 0.8065 (tpp) REVERT: A 353 LYS cc_start: 0.9025 (tttt) cc_final: 0.7919 (ttmt) REVERT: A 392 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8453 (mm) REVERT: A 398 GLU cc_start: 0.8278 (pt0) cc_final: 0.8058 (pt0) REVERT: A 481 LYS cc_start: 0.8850 (tppp) cc_final: 0.8520 (ttpt) REVERT: A 483 GLU cc_start: 0.9135 (tp30) cc_final: 0.8672 (mm-30) REVERT: A 565 PRO cc_start: 0.8848 (Cg_exo) cc_final: 0.8562 (Cg_endo) REVERT: A 567 THR cc_start: 0.9090 (m) cc_final: 0.8801 (p) REVERT: E 357 ARG cc_start: 0.8348 (ttt180) cc_final: 0.7099 (mtt180) REVERT: E 409 GLN cc_start: 0.9408 (mm110) cc_final: 0.9123 (mp10) REVERT: E 442 ASP cc_start: 0.8871 (m-30) cc_final: 0.7838 (m-30) REVERT: E 444 LYS cc_start: 0.8318 (ptmm) cc_final: 0.6791 (mttt) REVERT: E 473 TYR cc_start: 0.8727 (t80) cc_final: 0.8367 (t80) REVERT: E 507 PRO cc_start: 0.9126 (Cg_exo) cc_final: 0.8886 (Cg_endo) REVERT: E 509 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.8034 (mmt-90) outliers start: 16 outliers final: 13 residues processed: 163 average time/residue: 0.1921 time to fit residues: 41.3753 Evaluate side-chains 162 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 82 MET 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 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 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: 6.9990 chunk 11 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 0.0070 chunk 76 optimal weight: 0.3980 chunk 49 optimal weight: 0.3980 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 96 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.120839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.101223 restraints weight = 37347.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.106002 restraints weight = 15368.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.109164 restraints weight = 8397.475| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4859 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= 0.216 Angle : 0.761 11.327 9038 Z= 0.377 Chirality : 0.047 0.301 962 Planarity : 0.005 0.053 1166 Dihedral : 5.395 38.050 968 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.33 % Allowed : 23.14 % Favored : 74.53 % 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 (0.30), residues: 789 helix: 0.65 (0.26), residues: 391 sheet: -1.16 (0.70), residues: 53 loop : -1.17 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP A 168 HIS 0.006 0.001 HIS A 540 PHE 0.029 0.002 PHE A 274 TYR 0.032 0.002 TYR A 237 ARG 0.002 0.001 ARG A 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2599.22 seconds wall clock time: 45 minutes 42.51 seconds (2742.51 seconds total)