Starting phenix.real_space_refine on Thu Jul 24 20:07:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fdg_31542/07_2025/7fdg_31542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdg_31542/07_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_31542/07_2025/7fdg_31542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdg_31542/07_2025/7fdg_31542.map" model { file = "/net/cci-nas-00/data/ceres_data/7fdg_31542/07_2025/7fdg_31542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdg_31542/07_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-5711/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: 7.54, per 1000 atoms: 1.17 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: 1.45 Conformation dependent library (CDL) restraints added in 1.5 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: 0.60 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: 1.58 Time building geometry restraints manager: 1.75 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.880 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 6655 Z= 0.329 Angle : 0.870 9.117 9067 Z= 0.493 Chirality : 0.047 0.177 962 Planarity : 0.005 0.044 1166 Dihedral : 16.003 86.573 2465 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.29 % Allowed : 6.55 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 5) link_NAG-ASN : angle 3.92781 ( 15) hydrogen bonds : bond 0.14417 ( 322) hydrogen bonds : angle 6.69268 ( 916) SS BOND : bond 0.00709 ( 7) SS BOND : angle 3.08745 ( 14) covalent geometry : bond 0.00656 ( 6643) covalent geometry : angle 0.84766 ( 9038) *********************** 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 : 0.754 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: 0.1961 time to fit residues: 49.3297 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 : 0.720 ------------------------------------------------------------------------------- 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 6655 Z= 0.158 Angle : 0.756 8.412 9067 Z= 0.382 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 5) link_NAG-ASN : angle 3.59281 ( 15) hydrogen bonds : bond 0.04893 ( 322) hydrogen bonds : angle 5.30939 ( 916) SS BOND : bond 0.00646 ( 7) SS BOND : angle 2.43927 ( 14) covalent geometry : bond 0.00335 ( 6643) covalent geometry : angle 0.73641 ( 9038) *********************** 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 : 0.658 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: 0.1735 time to fit residues: 45.2230 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 : 0.614 ------------------------------------------------------------------------------- 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 6655 Z= 0.174 Angle : 0.749 9.225 9067 Z= 0.374 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 5) link_NAG-ASN : angle 3.05378 ( 15) hydrogen bonds : bond 0.04699 ( 322) hydrogen bonds : angle 5.14542 ( 916) SS BOND : bond 0.00521 ( 7) SS BOND : angle 2.56575 ( 14) covalent geometry : bond 0.00385 ( 6643) covalent geometry : angle 0.73331 ( 9038) *********************** 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 : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.1746 time to fit residues: 42.9146 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 : 0.741 ------------------------------------------------------------------------------- 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: 7.9990 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 6655 Z= 0.153 Angle : 0.728 9.303 9067 Z= 0.362 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 5) link_NAG-ASN : angle 2.72433 ( 15) hydrogen bonds : bond 0.04391 ( 322) hydrogen bonds : angle 5.05201 ( 916) SS BOND : bond 0.00605 ( 7) SS BOND : angle 2.28714 ( 14) covalent geometry : bond 0.00338 ( 6643) covalent geometry : angle 0.71489 ( 9038) *********************** 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 : 0.678 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: 0.1809 time to fit residues: 42.7759 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 : 0.671 ------------------------------------------------------------------------------- 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: 2.9990 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: 3.9990 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.0570 chunk 38 optimal weight: 10.0000 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 6655 Z= 0.136 Angle : 0.718 8.967 9067 Z= 0.357 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 5) link_NAG-ASN : angle 2.52866 ( 15) hydrogen bonds : bond 0.04275 ( 322) hydrogen bonds : angle 4.94566 ( 916) SS BOND : bond 0.00507 ( 7) SS BOND : angle 1.98176 ( 14) covalent geometry : bond 0.00300 ( 6643) covalent geometry : angle 0.70725 ( 9038) *********************** 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 : 0.614 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: 0.1727 time to fit residues: 40.6081 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 : 0.774 ------------------------------------------------------------------------------- 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: 1.9990 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.124990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.106662 restraints weight = 26446.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.110822 restraints weight = 12328.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.113636 restraints weight = 7143.596| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 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 = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6655 Z= 0.135 Angle : 0.719 9.397 9067 Z= 0.353 Chirality : 0.044 0.237 962 Planarity : 0.005 0.052 1166 Dihedral : 5.539 38.822 968 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.33 % Allowed : 21.40 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.30), residues: 789 helix: 0.71 (0.26), residues: 397 sheet: -1.06 (0.68), residues: 55 loop : -1.23 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 477 HIS 0.004 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 5) link_NAG-ASN : angle 2.56591 ( 15) hydrogen bonds : bond 0.04174 ( 322) hydrogen bonds : angle 4.86781 ( 916) SS BOND : bond 0.00446 ( 7) SS BOND : angle 1.92995 ( 14) covalent geometry : bond 0.00302 ( 6643) covalent geometry : angle 0.70897 ( 9038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.874 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: 0.8865 (t80) cc_final: 0.8417 (t80) REVERT: A 75 GLU cc_start: 0.8581 (pp20) cc_final: 0.8034 (pp20) REVERT: A 76 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8883 (mm-40) REVERT: A 258 PRO cc_start: 0.7655 (Cg_endo) cc_final: 0.7163 (Cg_exo) REVERT: A 323 MET cc_start: 0.7699 (mmm) cc_final: 0.6816 (mmm) REVERT: A 353 LYS cc_start: 0.8925 (mttt) cc_final: 0.7951 (ttmt) REVERT: A 376 MET cc_start: 0.8814 (tpt) cc_final: 0.8523 (tpp) REVERT: A 392 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 398 GLU cc_start: 0.8232 (pt0) cc_final: 0.7958 (pt0) REVERT: A 406 GLU cc_start: 0.8730 (tt0) cc_final: 0.8320 (tt0) REVERT: A 481 LYS cc_start: 0.8904 (tppp) cc_final: 0.8562 (ttpt) REVERT: A 483 GLU cc_start: 0.9144 (tp30) cc_final: 0.8694 (mm-30) REVERT: A 499 ASP cc_start: 0.8641 (m-30) cc_final: 0.8071 (t0) REVERT: A 565 PRO cc_start: 0.8686 (Cg_exo) cc_final: 0.8365 (Cg_endo) REVERT: A 567 THR cc_start: 0.9080 (m) cc_final: 0.8806 (p) REVERT: E 357 ARG cc_start: 0.8369 (ttt180) cc_final: 0.7045 (mtt180) REVERT: E 409 GLN cc_start: 0.9383 (mm110) cc_final: 0.9122 (mp10) REVERT: E 442 ASP cc_start: 0.8988 (m-30) cc_final: 0.8243 (m-30) REVERT: E 444 LYS cc_start: 0.8213 (ptmm) cc_final: 0.6642 (mttt) REVERT: E 473 TYR cc_start: 0.8575 (t80) cc_final: 0.8118 (t80) outliers start: 15 outliers final: 11 residues processed: 173 average time/residue: 0.1771 time to fit residues: 40.7604 Evaluate side-chains 162 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 530 CYS Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.2762 ------------------------------------------------------------------------------- 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 ** 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 = 0.4008 r_free = 0.4008 target = 0.122019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.102372 restraints weight = 45828.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.107424 restraints weight = 16893.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.110731 restraints weight = 8742.794| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6655 Z= 0.146 Angle : 0.740 10.572 9067 Z= 0.363 Chirality : 0.045 0.223 962 Planarity : 0.005 0.052 1166 Dihedral : 5.449 37.615 968 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.77 % Allowed : 21.40 % Favored : 75.84 % 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: -0.35 (0.30), residues: 789 helix: 0.78 (0.26), residues: 390 sheet: -1.15 (0.67), residues: 59 loop : -1.22 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 477 HIS 0.005 0.001 HIS A 34 PHE 0.042 0.002 PHE E 456 TYR 0.028 0.002 TYR A 381 ARG 0.004 0.001 ARG E 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 5) link_NAG-ASN : angle 2.49077 ( 15) hydrogen bonds : bond 0.04215 ( 322) hydrogen bonds : angle 4.88860 ( 916) SS BOND : bond 0.00428 ( 7) SS BOND : angle 2.02871 ( 14) covalent geometry : bond 0.00326 ( 6643) covalent geometry : angle 0.73002 ( 9038) *********************** 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 172 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.721 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: 0.8903 (t80) cc_final: 0.8505 (t80) REVERT: A 75 GLU cc_start: 0.8568 (pp20) cc_final: 0.8009 (pp20) REVERT: A 76 GLN cc_start: 0.9260 (mm-40) cc_final: 0.8897 (mm-40) REVERT: A 127 TYR cc_start: 0.7336 (t80) cc_final: 0.7116 (t80) REVERT: A 258 PRO cc_start: 0.7435 (Cg_endo) cc_final: 0.7161 (Cg_exo) REVERT: A 323 MET cc_start: 0.7692 (mmm) cc_final: 0.6697 (mmm) REVERT: A 353 LYS cc_start: 0.8981 (mttt) cc_final: 0.7991 (ttmt) REVERT: A 392 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8503 (mm) REVERT: A 398 GLU cc_start: 0.8214 (pt0) cc_final: 0.7895 (pt0) REVERT: A 406 GLU cc_start: 0.8888 (tt0) cc_final: 0.8469 (tt0) REVERT: A 430 GLU cc_start: 0.7729 (tp30) cc_final: 0.7519 (tp30) REVERT: A 481 LYS cc_start: 0.8892 (tppp) cc_final: 0.8518 (ttpt) REVERT: A 483 GLU cc_start: 0.9138 (tp30) cc_final: 0.8697 (mm-30) REVERT: A 499 ASP cc_start: 0.8483 (m-30) cc_final: 0.7515 (t0) REVERT: A 565 PRO cc_start: 0.8727 (Cg_exo) cc_final: 0.8426 (Cg_endo) REVERT: A 567 THR cc_start: 0.9069 (m) cc_final: 0.8805 (p) REVERT: E 357 ARG cc_start: 0.8347 (ttt180) cc_final: 0.7058 (mtt180) REVERT: E 409 GLN cc_start: 0.9427 (mm110) cc_final: 0.9154 (mp10) REVERT: E 442 ASP cc_start: 0.8876 (m-30) cc_final: 0.7994 (m-30) REVERT: E 444 LYS cc_start: 0.8305 (ptmm) cc_final: 0.6756 (mttt) REVERT: E 509 ARG cc_start: 0.8537 (mmt90) cc_final: 0.7820 (mmm-85) outliers start: 18 outliers final: 11 residues processed: 166 average time/residue: 0.2188 time to fit residues: 48.3542 Evaluate side-chains 160 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 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 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 12 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN E 422 ASN E 481 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.123908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.104194 restraints weight = 44791.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.109204 restraints weight = 16766.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.112514 restraints weight = 8788.718| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6655 Z= 0.136 Angle : 0.740 9.618 9067 Z= 0.364 Chirality : 0.045 0.186 962 Planarity : 0.005 0.053 1166 Dihedral : 5.300 37.062 968 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.91 % Allowed : 21.25 % Favored : 75.84 % 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: -0.45 (0.30), residues: 789 helix: 0.65 (0.26), residues: 393 sheet: -1.10 (0.68), residues: 59 loop : -1.24 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 168 HIS 0.004 0.001 HIS A 241 PHE 0.022 0.001 PHE A 230 TYR 0.057 0.002 TYR A 237 ARG 0.005 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 5) link_NAG-ASN : angle 2.44923 ( 15) hydrogen bonds : bond 0.04222 ( 322) hydrogen bonds : angle 4.88303 ( 916) SS BOND : bond 0.00427 ( 7) SS BOND : angle 1.82293 ( 14) covalent geometry : bond 0.00302 ( 6643) covalent geometry : angle 0.73128 ( 9038) *********************** 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 177 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.758 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 62 MET cc_start: 0.9237 (ttp) cc_final: 0.8305 (ttt) REVERT: A 72 PHE cc_start: 0.8879 (t80) cc_final: 0.8460 (t80) REVERT: A 75 GLU cc_start: 0.8571 (pp20) cc_final: 0.8029 (pp20) REVERT: A 76 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8878 (mm-40) REVERT: A 213 ASP cc_start: 0.8425 (t70) cc_final: 0.8192 (m-30) REVERT: A 258 PRO cc_start: 0.7424 (Cg_endo) cc_final: 0.7156 (Cg_exo) REVERT: A 323 MET cc_start: 0.7809 (mmm) cc_final: 0.6954 (mmm) REVERT: A 353 LYS cc_start: 0.8948 (mttt) cc_final: 0.7988 (ttmt) REVERT: A 392 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8507 (mm) REVERT: A 398 GLU cc_start: 0.8112 (pt0) cc_final: 0.7792 (pt0) REVERT: A 481 LYS cc_start: 0.8882 (tppp) cc_final: 0.8552 (ttpt) REVERT: A 483 GLU cc_start: 0.9122 (tp30) cc_final: 0.8678 (mm-30) REVERT: A 565 PRO cc_start: 0.8683 (Cg_exo) cc_final: 0.8395 (Cg_endo) REVERT: E 357 ARG cc_start: 0.8313 (ttt180) cc_final: 0.7004 (mtt180) REVERT: E 409 GLN cc_start: 0.9427 (mm110) cc_final: 0.9168 (mp10) REVERT: E 442 ASP cc_start: 0.8849 (m-30) cc_final: 0.8469 (m-30) REVERT: E 444 LYS cc_start: 0.8244 (ptmm) cc_final: 0.6675 (mttt) outliers start: 19 outliers final: 13 residues processed: 167 average time/residue: 0.1924 time to fit residues: 42.8627 Evaluate side-chains 168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 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 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: 0.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** E 360 ASN E 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.124282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.103675 restraints weight = 50036.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.108954 restraints weight = 18086.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.112435 restraints weight = 9362.933| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6655 Z= 0.145 Angle : 0.752 10.941 9067 Z= 0.369 Chirality : 0.045 0.176 962 Planarity : 0.005 0.052 1166 Dihedral : 5.263 35.849 968 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.62 % Allowed : 23.00 % Favored : 74.38 % 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: -0.56 (0.30), residues: 789 helix: 0.50 (0.26), residues: 398 sheet: -1.19 (0.68), residues: 59 loop : -1.23 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 168 HIS 0.003 0.001 HIS A 505 PHE 0.021 0.002 PHE A 230 TYR 0.027 0.002 TYR A 237 ARG 0.004 0.001 ARG E 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 5) link_NAG-ASN : angle 2.35688 ( 15) hydrogen bonds : bond 0.04240 ( 322) hydrogen bonds : angle 4.87774 ( 916) SS BOND : bond 0.00396 ( 7) SS BOND : angle 1.78769 ( 14) covalent geometry : bond 0.00323 ( 6643) covalent geometry : angle 0.74382 ( 9038) *********************** 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 171 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.883 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 62 MET cc_start: 0.9253 (ttp) cc_final: 0.8326 (ttt) REVERT: A 72 PHE cc_start: 0.8870 (t80) cc_final: 0.8451 (t80) REVERT: A 75 GLU cc_start: 0.8563 (pp20) cc_final: 0.8022 (pp20) REVERT: A 76 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8950 (mm-40) REVERT: A 258 PRO cc_start: 0.7486 (Cg_endo) cc_final: 0.7235 (Cg_exo) REVERT: A 353 LYS cc_start: 0.8978 (mttt) cc_final: 0.8037 (ttmt) REVERT: A 392 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 398 GLU cc_start: 0.8221 (pt0) cc_final: 0.7874 (pt0) REVERT: A 481 LYS cc_start: 0.8882 (tppp) cc_final: 0.8514 (ttpt) REVERT: A 483 GLU cc_start: 0.9118 (tp30) cc_final: 0.8677 (mm-30) REVERT: A 565 PRO cc_start: 0.8724 (Cg_exo) cc_final: 0.8438 (Cg_endo) REVERT: E 357 ARG cc_start: 0.8286 (ttt180) cc_final: 0.7005 (mtt180) REVERT: E 409 GLN cc_start: 0.9419 (mm110) cc_final: 0.9169 (mp10) REVERT: E 442 ASP cc_start: 0.8877 (m-30) cc_final: 0.8358 (m-30) REVERT: E 444 LYS cc_start: 0.8335 (ptmm) cc_final: 0.6765 (mttt) outliers start: 17 outliers final: 14 residues processed: 162 average time/residue: 0.2226 time to fit residues: 48.6689 Evaluate side-chains 165 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 224 GLU 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 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: 5.9990 chunk 22 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** E 481 ASN E 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.121545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.104001 restraints weight = 25276.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.108053 restraints weight = 12075.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.110762 restraints weight = 7054.464| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6655 Z= 0.144 Angle : 0.763 10.709 9067 Z= 0.376 Chirality : 0.045 0.187 962 Planarity : 0.005 0.051 1166 Dihedral : 5.230 35.022 968 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.47 % Allowed : 23.14 % Favored : 74.38 % 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: -0.55 (0.30), residues: 789 helix: 0.49 (0.26), residues: 399 sheet: -1.13 (0.68), residues: 59 loop : -1.21 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 168 HIS 0.008 0.001 HIS A 540 PHE 0.027 0.002 PHE E 456 TYR 0.027 0.002 TYR A 381 ARG 0.006 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 5) link_NAG-ASN : angle 2.32575 ( 15) hydrogen bonds : bond 0.04242 ( 322) hydrogen bonds : angle 4.92730 ( 916) SS BOND : bond 0.00393 ( 7) SS BOND : angle 1.85273 ( 14) covalent geometry : bond 0.00321 ( 6643) covalent geometry : angle 0.75491 ( 9038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.755 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: 0.9258 (ttp) cc_final: 0.8333 (ttt) REVERT: A 72 PHE cc_start: 0.8874 (t80) cc_final: 0.8441 (t80) REVERT: A 75 GLU cc_start: 0.8531 (pp20) cc_final: 0.7994 (pp20) REVERT: A 76 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8943 (mm-40) REVERT: A 258 PRO cc_start: 0.7489 (Cg_endo) cc_final: 0.7240 (Cg_exo) REVERT: A 353 LYS cc_start: 0.8989 (mttt) cc_final: 0.8008 (ttmt) REVERT: A 392 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8427 (mm) REVERT: A 398 GLU cc_start: 0.8155 (pt0) cc_final: 0.7641 (pt0) REVERT: A 406 GLU cc_start: 0.8836 (tt0) cc_final: 0.8226 (tt0) REVERT: A 481 LYS cc_start: 0.8879 (tppp) cc_final: 0.8554 (ttpt) REVERT: A 483 GLU cc_start: 0.9131 (tp30) cc_final: 0.8686 (mm-30) REVERT: A 565 PRO cc_start: 0.8753 (Cg_exo) cc_final: 0.8470 (Cg_endo) REVERT: A 567 THR cc_start: 0.9113 (m) cc_final: 0.8850 (p) REVERT: E 357 ARG cc_start: 0.8257 (ttt180) cc_final: 0.7008 (mtt180) REVERT: E 442 ASP cc_start: 0.8916 (m-30) cc_final: 0.8441 (m-30) REVERT: E 444 LYS cc_start: 0.8335 (ptmm) cc_final: 0.6793 (mttt) outliers start: 16 outliers final: 12 residues processed: 164 average time/residue: 0.2167 time to fit residues: 47.9188 Evaluate side-chains 163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 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: 5.9990 chunk 11 optimal weight: 20.0000 chunk 25 optimal weight: 0.0020 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 0.0970 chunk 38 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.123282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.103512 restraints weight = 37549.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.108366 restraints weight = 15616.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.111559 restraints weight = 8538.359| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6655 Z= 0.146 Angle : 0.781 12.110 9067 Z= 0.388 Chirality : 0.046 0.260 962 Planarity : 0.005 0.052 1166 Dihedral : 5.172 33.950 968 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.04 % Allowed : 23.58 % Favored : 74.38 % 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: -0.61 (0.30), residues: 789 helix: 0.35 (0.26), residues: 413 sheet: -1.05 (0.70), residues: 57 loop : -1.21 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 168 HIS 0.007 0.001 HIS A 540 PHE 0.020 0.001 PHE A 369 TYR 0.026 0.002 TYR A 381 ARG 0.004 0.001 ARG E 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 5) link_NAG-ASN : angle 2.22161 ( 15) hydrogen bonds : bond 0.04236 ( 322) hydrogen bonds : angle 4.92293 ( 916) SS BOND : bond 0.00417 ( 7) SS BOND : angle 1.82046 ( 14) covalent geometry : bond 0.00327 ( 6643) covalent geometry : angle 0.77405 ( 9038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3403.34 seconds wall clock time: 61 minutes 55.20 seconds (3715.20 seconds total)