Starting phenix.real_space_refine on Mon Apr 28 17:53:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ten_41192/04_2025/8ten_41192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ten_41192/04_2025/8ten_41192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ten_41192/04_2025/8ten_41192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ten_41192/04_2025/8ten_41192.map" model { file = "/net/cci-nas-00/data/ceres_data/8ten_41192/04_2025/8ten_41192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ten_41192/04_2025/8ten_41192.cif" } resolution = 2.98 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= 0.002 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 55 5.16 5 C 5187 2.51 5 N 1288 2.21 5 O 1341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7872 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3903 Classifications: {'peptide': 494} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 467} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3969 Classifications: {'peptide': 502} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 471} Chain breaks: 2 Time building chain proxies: 5.76, per 1000 atoms: 0.73 Number of scatterers: 7872 At special positions: 0 Unit cell: (90.47, 120.35, 95.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 1 15.00 O 1341 8.00 N 1288 7.00 C 5187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 80.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 removed outlier: 3.994A pdb=" N MET A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.786A pdb=" N ALA A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 36 through 62 Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.783A pdb=" N ALA A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 145 through 151 removed outlier: 4.050A pdb=" N ASN A 149 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 178 removed outlier: 4.048A pdb=" N PHE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 219 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 228 through 251 removed outlier: 6.500A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 252 through 258 removed outlier: 4.462A pdb=" N GLY A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.543A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 297 through 319 removed outlier: 3.567A pdb=" N SER A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 359 through 391 removed outlier: 3.663A pdb=" N LYS A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 442 through 446 Processing helix chain 'A' and resid 447 through 453 removed outlier: 4.060A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 464 through 480 removed outlier: 3.916A pdb=" N VAL A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.722A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 36 through 62 removed outlier: 3.979A pdb=" N ILE B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 67 through 86 Processing helix chain 'B' and resid 96 through 113 removed outlier: 3.738A pdb=" N ALA B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 142 Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.521A pdb=" N SER B 146 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASN B 149 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 178 removed outlier: 3.575A pdb=" N GLY B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 192 Processing helix chain 'B' and resid 193 through 219 Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.560A pdb=" N SER B 223 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 252 removed outlier: 6.589A pdb=" N VAL B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.532A pdb=" N VAL B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.513A pdb=" N LEU B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 297 through 320 removed outlier: 3.830A pdb=" N SER B 313 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'B' and resid 359 through 368 Processing helix chain 'B' and resid 464 through 477 removed outlier: 3.603A pdb=" N LEU B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 Processing helix chain 'B' and resid 488 through 503 removed outlier: 3.716A pdb=" N LEU B 492 " --> pdb=" O PRO B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 517 Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 529 removed outlier: 3.701A pdb=" N VAL B 526 " --> pdb=" O ARG B 522 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 529 " --> pdb=" O LYS B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 539 through 562 removed outlier: 3.670A pdb=" N TRP B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 569 through 589 removed outlier: 3.548A pdb=" N MET B 573 " --> pdb=" O MET B 569 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 577 " --> pdb=" O MET B 573 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix removed outlier: 4.497A pdb=" N LEU B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) Proline residue: B 586 - end of helix Processing helix chain 'B' and resid 591 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA2, first strand: chain 'B' and resid 93 through 94 529 hydrogen bonds defined for protein. 1524 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: 2.61 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2409 1.34 - 1.46: 1442 1.46 - 1.58: 4129 1.58 - 1.70: 3 1.70 - 1.81: 95 Bond restraints: 8078 Sorted by residual: bond pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" O3P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" O2P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O1P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.525 1.478 0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" N TPO A 410 " pdb=" CA TPO A 410 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.22e+00 ... (remaining 8073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 10843 2.01 - 4.03: 107 4.03 - 6.04: 13 6.04 - 8.06: 0 8.06 - 10.07: 2 Bond angle restraints: 10965 Sorted by residual: angle pdb=" CB TPO A 410 " pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 119.31 109.24 10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " pdb=" O1P TPO A 410 " ideal model delta sigma weight residual 100.43 109.58 -9.15 3.00e+00 1.11e-01 9.31e+00 angle pdb=" CA PRO A 417 " pdb=" N PRO A 417 " pdb=" CD PRO A 417 " ideal model delta sigma weight residual 112.00 108.46 3.54 1.40e+00 5.10e-01 6.40e+00 angle pdb=" N LEU B 504 " pdb=" CA LEU B 504 " pdb=" C LEU B 504 " ideal model delta sigma weight residual 109.81 115.11 -5.30 2.21e+00 2.05e-01 5.74e+00 angle pdb=" O1P TPO A 410 " pdb=" P TPO A 410 " pdb=" O2P TPO A 410 " ideal model delta sigma weight residual 114.94 109.27 5.67 3.00e+00 1.11e-01 3.57e+00 ... (remaining 10960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4073 17.49 - 34.97: 487 34.97 - 52.46: 153 52.46 - 69.95: 28 69.95 - 87.44: 16 Dihedral angle restraints: 4757 sinusoidal: 1895 harmonic: 2862 Sorted by residual: dihedral pdb=" CA ILE A 291 " pdb=" C ILE A 291 " pdb=" N VAL A 292 " pdb=" CA VAL A 292 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LYS B 590 " pdb=" C LYS B 590 " pdb=" N GLY B 591 " pdb=" CA GLY B 591 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLY A 395 " pdb=" C GLY A 395 " pdb=" N GLN A 396 " pdb=" CA GLN A 396 " ideal model delta harmonic sigma weight residual 180.00 161.12 18.88 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 825 0.030 - 0.059: 277 0.059 - 0.089: 93 0.089 - 0.118: 33 0.118 - 0.148: 15 Chirality restraints: 1243 Sorted by residual: chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE A 181 " pdb=" N ILE A 181 " pdb=" C ILE A 181 " pdb=" CB ILE A 181 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CB THR A 390 " pdb=" CA THR A 390 " pdb=" OG1 THR A 390 " pdb=" CG2 THR A 390 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1240 not shown) Planarity restraints: 1359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 416 " -0.065 5.00e-02 4.00e+02 9.70e-02 1.50e+01 pdb=" N PRO A 417 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 417 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 417 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 563 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 564 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 564 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 564 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 97 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO B 98 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " 0.017 5.00e-02 4.00e+02 ... (remaining 1356 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 73 2.64 - 3.21: 7501 3.21 - 3.77: 12286 3.77 - 4.34: 16860 4.34 - 4.90: 27783 Nonbonded interactions: 64503 Sorted by model distance: nonbonded pdb=" OH TYR A 405 " pdb=" OE2 GLU A 459 " model vdw 2.079 3.040 nonbonded pdb=" O ALA B 144 " pdb=" OH TYR B 309 " model vdw 2.102 3.040 nonbonded pdb=" O GLY A 227 " pdb=" NH1 ARG A 232 " model vdw 2.169 3.120 nonbonded pdb=" O LEU B 58 " pdb=" OG1 THR B 62 " model vdw 2.267 3.040 nonbonded pdb=" O SER A 223 " pdb=" OG SER A 223 " model vdw 2.294 3.040 ... (remaining 64498 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 1.860 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.100 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 0.003 0.107 8078 Z= 0.155 Angle : 0.544 10.072 10965 Z= 0.272 Chirality : 0.037 0.148 1243 Planarity : 0.005 0.097 1359 Dihedral : 17.493 87.436 2917 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.07 % Allowed : 21.26 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 2.34 (0.27), residues: 981 helix: 2.06 (0.20), residues: 699 sheet: None (None), residues: 0 loop : 0.35 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 230 HIS 0.002 0.001 HIS A 333 PHE 0.008 0.001 PHE B 570 TYR 0.009 0.001 TYR A 495 ARG 0.007 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.12979 ( 529) hydrogen bonds : angle 4.97409 ( 1524) covalent geometry : bond 0.00331 ( 8078) covalent geometry : angle 0.54403 (10965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.842 Fit side-chains REVERT: A 23 LYS cc_start: 0.7292 (mmtt) cc_final: 0.6741 (tttm) REVERT: A 234 LEU cc_start: 0.8305 (mp) cc_final: 0.7923 (tt) REVERT: A 260 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7312 (mptt) REVERT: A 345 MET cc_start: 0.9029 (ttp) cc_final: 0.8595 (ttp) REVERT: B 345 MET cc_start: 0.7989 (ttm) cc_final: 0.7746 (tmm) outliers start: 9 outliers final: 6 residues processed: 105 average time/residue: 1.2632 time to fit residues: 140.6623 Evaluate side-chains 96 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.171213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128578 restraints weight = 8824.920| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.83 r_work: 0.3180 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8078 Z= 0.125 Angle : 0.524 6.949 10965 Z= 0.264 Chirality : 0.040 0.183 1243 Planarity : 0.004 0.073 1359 Dihedral : 4.608 32.240 1085 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.44 % Allowed : 18.17 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 2.48 (0.27), residues: 981 helix: 2.09 (0.20), residues: 713 sheet: None (None), residues: 0 loop : 0.56 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.003 0.001 HIS B 312 PHE 0.009 0.001 PHE B 534 TYR 0.008 0.001 TYR B 22 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 529) hydrogen bonds : angle 4.26031 ( 1524) covalent geometry : bond 0.00268 ( 8078) covalent geometry : angle 0.52443 (10965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.818 Fit side-chains REVERT: A 23 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6553 (tttm) REVERT: A 234 LEU cc_start: 0.8217 (mp) cc_final: 0.7927 (tt) REVERT: A 345 MET cc_start: 0.8920 (ttp) cc_final: 0.8479 (ttp) REVERT: B 231 LEU cc_start: 0.6291 (tt) cc_final: 0.6006 (tt) REVERT: B 235 ILE cc_start: 0.7390 (mt) cc_final: 0.7021 (mt) REVERT: B 516 LEU cc_start: 0.7431 (tt) cc_final: 0.7204 (tp) REVERT: B 548 LEU cc_start: 0.6764 (mp) cc_final: 0.6503 (mt) outliers start: 29 outliers final: 12 residues processed: 122 average time/residue: 1.1557 time to fit residues: 149.9295 Evaluate side-chains 113 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 596 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 64 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 90 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 chunk 49 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.172213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130361 restraints weight = 8934.375| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.88 r_work: 0.3122 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8078 Z= 0.136 Angle : 0.532 6.787 10965 Z= 0.265 Chirality : 0.040 0.160 1243 Planarity : 0.005 0.066 1359 Dihedral : 4.261 31.460 1075 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.16 % Allowed : 18.65 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 2.42 (0.27), residues: 981 helix: 2.12 (0.19), residues: 699 sheet: None (None), residues: 0 loop : 0.37 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.003 0.001 HIS A 333 PHE 0.019 0.001 PHE B 310 TYR 0.010 0.001 TYR B 103 ARG 0.004 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 529) hydrogen bonds : angle 4.22032 ( 1524) covalent geometry : bond 0.00313 ( 8078) covalent geometry : angle 0.53168 (10965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7422 (mmtt) cc_final: 0.6699 (tttm) REVERT: A 181 ILE cc_start: 0.6458 (OUTLIER) cc_final: 0.5967 (mm) REVERT: A 234 LEU cc_start: 0.8282 (mp) cc_final: 0.7994 (tt) REVERT: A 345 MET cc_start: 0.8969 (ttp) cc_final: 0.8537 (ttp) REVERT: B 228 THR cc_start: 0.4629 (OUTLIER) cc_final: 0.4389 (t) REVERT: B 463 GLN cc_start: 0.2831 (OUTLIER) cc_final: 0.2592 (mm110) REVERT: B 548 LEU cc_start: 0.6769 (mp) cc_final: 0.6478 (mt) REVERT: B 598 ASP cc_start: 0.4973 (t70) cc_final: 0.4735 (t70) outliers start: 35 outliers final: 14 residues processed: 125 average time/residue: 1.2351 time to fit residues: 164.4703 Evaluate side-chains 115 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 596 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.169753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.127393 restraints weight = 8854.638| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.16 r_work: 0.3082 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8078 Z= 0.172 Angle : 0.578 7.010 10965 Z= 0.288 Chirality : 0.042 0.150 1243 Planarity : 0.005 0.064 1359 Dihedral : 4.476 31.548 1074 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.51 % Allowed : 19.48 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 2.07 (0.27), residues: 981 helix: 1.87 (0.19), residues: 697 sheet: None (None), residues: 0 loop : 0.22 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.004 0.001 HIS A 333 PHE 0.011 0.002 PHE B 30 TYR 0.011 0.002 TYR B 103 ARG 0.004 0.001 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05424 ( 529) hydrogen bonds : angle 4.32930 ( 1524) covalent geometry : bond 0.00412 ( 8078) covalent geometry : angle 0.57807 (10965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7267 (mmtt) cc_final: 0.6494 (tttm) REVERT: A 181 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.5858 (mm) REVERT: A 183 GLU cc_start: 0.5326 (OUTLIER) cc_final: 0.5115 (mm-30) REVERT: A 188 LYS cc_start: 0.5165 (mmpt) cc_final: 0.4783 (mppt) REVERT: A 286 MET cc_start: 0.8075 (mtp) cc_final: 0.7837 (mtm) REVERT: A 345 MET cc_start: 0.8963 (ttp) cc_final: 0.8540 (ttp) REVERT: A 386 ARG cc_start: 0.7401 (tpt-90) cc_final: 0.6501 (tpp80) REVERT: A 459 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7783 (mt-10) REVERT: A 463 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7521 (pp30) REVERT: B 80 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5871 (ptt) REVERT: B 177 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: B 219 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7350 (mmm-85) REVERT: B 228 THR cc_start: 0.4924 (OUTLIER) cc_final: 0.4685 (t) REVERT: B 322 LYS cc_start: 0.3178 (OUTLIER) cc_final: 0.2962 (pttm) REVERT: B 548 LEU cc_start: 0.6756 (mp) cc_final: 0.6452 (mt) outliers start: 38 outliers final: 18 residues processed: 128 average time/residue: 1.2452 time to fit residues: 168.8273 Evaluate side-chains 122 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 596 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 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 = 0.3931 r_free = 0.3931 target = 0.171445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129926 restraints weight = 8811.758| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.77 r_work: 0.3148 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8078 Z= 0.121 Angle : 0.523 8.260 10965 Z= 0.257 Chirality : 0.039 0.144 1243 Planarity : 0.004 0.060 1359 Dihedral : 4.296 31.890 1074 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.44 % Allowed : 21.50 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 2.42 (0.27), residues: 981 helix: 2.14 (0.20), residues: 693 sheet: None (None), residues: 0 loop : 0.35 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 247 HIS 0.003 0.001 HIS B 312 PHE 0.023 0.001 PHE B 310 TYR 0.007 0.001 TYR B 103 ARG 0.003 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 529) hydrogen bonds : angle 4.13490 ( 1524) covalent geometry : bond 0.00274 ( 8078) covalent geometry : angle 0.52286 (10965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7274 (mmtt) cc_final: 0.6526 (tttm) REVERT: A 35 ARG cc_start: 0.6257 (mmp-170) cc_final: 0.5858 (mtt90) REVERT: A 181 ILE cc_start: 0.6424 (OUTLIER) cc_final: 0.5900 (mm) REVERT: A 188 LYS cc_start: 0.5240 (mmtt) cc_final: 0.4771 (mppt) REVERT: A 220 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8365 (mttp) REVERT: A 234 LEU cc_start: 0.8241 (mp) cc_final: 0.7901 (tt) REVERT: A 286 MET cc_start: 0.8084 (mtp) cc_final: 0.7837 (mtm) REVERT: A 345 MET cc_start: 0.8932 (ttp) cc_final: 0.8522 (ttp) REVERT: A 386 ARG cc_start: 0.7425 (tpt-90) cc_final: 0.6456 (tpp80) REVERT: A 459 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 183 GLU cc_start: 0.5691 (mt-10) cc_final: 0.5469 (mp0) REVERT: B 219 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7321 (mmm-85) REVERT: B 285 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6364 (mp0) REVERT: B 548 LEU cc_start: 0.6695 (mp) cc_final: 0.6400 (mt) outliers start: 29 outliers final: 17 residues processed: 127 average time/residue: 1.2532 time to fit residues: 168.5694 Evaluate side-chains 118 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 596 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 70 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 18 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN B 320 GLN ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.172491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130588 restraints weight = 8801.738| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.78 r_work: 0.3140 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8078 Z= 0.110 Angle : 0.500 6.885 10965 Z= 0.245 Chirality : 0.038 0.144 1243 Planarity : 0.004 0.056 1359 Dihedral : 4.140 32.200 1074 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.44 % Allowed : 22.33 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 2.61 (0.27), residues: 981 helix: 2.28 (0.20), residues: 695 sheet: None (None), residues: 0 loop : 0.44 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 247 HIS 0.003 0.001 HIS B 312 PHE 0.011 0.001 PHE B 570 TYR 0.007 0.001 TYR A 495 ARG 0.003 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 529) hydrogen bonds : angle 4.01630 ( 1524) covalent geometry : bond 0.00239 ( 8078) covalent geometry : angle 0.49999 (10965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7297 (mmtt) cc_final: 0.6540 (tttm) REVERT: A 35 ARG cc_start: 0.6300 (mmp-170) cc_final: 0.5821 (mtt90) REVERT: A 181 ILE cc_start: 0.6378 (OUTLIER) cc_final: 0.5764 (mm) REVERT: A 188 LYS cc_start: 0.5297 (mmtt) cc_final: 0.4758 (mppt) REVERT: A 220 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8374 (mttp) REVERT: A 234 LEU cc_start: 0.8201 (mp) cc_final: 0.7857 (tt) REVERT: A 286 MET cc_start: 0.8097 (mtp) cc_final: 0.7848 (mtm) REVERT: A 345 MET cc_start: 0.8932 (ttp) cc_final: 0.8510 (ttp) REVERT: A 386 ARG cc_start: 0.7458 (tpt-90) cc_final: 0.6451 (tpp80) REVERT: B 183 GLU cc_start: 0.5717 (mt-10) cc_final: 0.5516 (mp0) REVERT: B 219 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7246 (mmm-85) REVERT: B 548 LEU cc_start: 0.6707 (mp) cc_final: 0.6401 (mt) outliers start: 29 outliers final: 16 residues processed: 120 average time/residue: 1.2316 time to fit residues: 156.5397 Evaluate side-chains 115 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 507 ASN Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 596 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 0.0000 chunk 95 optimal weight: 0.0870 chunk 96 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.170847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129554 restraints weight = 8907.860| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.94 r_work: 0.3123 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8078 Z= 0.128 Angle : 0.528 7.347 10965 Z= 0.259 Chirality : 0.040 0.141 1243 Planarity : 0.004 0.057 1359 Dihedral : 4.189 31.375 1074 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.44 % Allowed : 22.33 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 2.50 (0.27), residues: 981 helix: 2.22 (0.20), residues: 694 sheet: None (None), residues: 0 loop : 0.34 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.003 0.001 HIS B 312 PHE 0.024 0.001 PHE B 310 TYR 0.008 0.001 TYR A 495 ARG 0.006 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 529) hydrogen bonds : angle 4.08780 ( 1524) covalent geometry : bond 0.00297 ( 8078) covalent geometry : angle 0.52847 (10965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7402 (mmtt) cc_final: 0.6680 (tttm) REVERT: A 35 ARG cc_start: 0.6413 (mmp-170) cc_final: 0.5961 (mtt90) REVERT: A 181 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.5977 (mm) REVERT: A 188 LYS cc_start: 0.5291 (mmtt) cc_final: 0.4751 (mppt) REVERT: A 220 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8452 (mttp) REVERT: A 234 LEU cc_start: 0.8272 (mp) cc_final: 0.7949 (tt) REVERT: A 286 MET cc_start: 0.8182 (mtp) cc_final: 0.7829 (mtm) REVERT: A 345 MET cc_start: 0.8990 (ttp) cc_final: 0.8554 (ttp) REVERT: A 386 ARG cc_start: 0.7466 (tpt-90) cc_final: 0.6457 (tpp80) REVERT: A 463 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7440 (pp30) REVERT: B 219 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7357 (mmm-85) REVERT: B 548 LEU cc_start: 0.6860 (mp) cc_final: 0.6647 (mp) REVERT: B 569 MET cc_start: 0.7224 (mtp) cc_final: 0.6981 (mtp) outliers start: 29 outliers final: 18 residues processed: 119 average time/residue: 1.1553 time to fit residues: 146.1184 Evaluate side-chains 114 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 596 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.170640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129539 restraints weight = 8954.237| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.86 r_work: 0.3159 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8078 Z= 0.111 Angle : 0.512 7.831 10965 Z= 0.249 Chirality : 0.039 0.143 1243 Planarity : 0.004 0.054 1359 Dihedral : 4.090 32.284 1074 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.21 % Allowed : 22.33 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 2.69 (0.27), residues: 981 helix: 2.33 (0.20), residues: 695 sheet: None (None), residues: 0 loop : 0.48 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 247 HIS 0.003 0.001 HIS B 312 PHE 0.011 0.001 PHE B 298 TYR 0.007 0.001 TYR A 495 ARG 0.004 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 529) hydrogen bonds : angle 3.98598 ( 1524) covalent geometry : bond 0.00245 ( 8078) covalent geometry : angle 0.51178 (10965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7359 (mmtt) cc_final: 0.6628 (tttm) REVERT: A 35 ARG cc_start: 0.6388 (mmp-170) cc_final: 0.5918 (mtt90) REVERT: A 181 ILE cc_start: 0.6457 (OUTLIER) cc_final: 0.5907 (mm) REVERT: A 188 LYS cc_start: 0.5303 (mmtt) cc_final: 0.4721 (mppt) REVERT: A 220 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8442 (mttp) REVERT: A 234 LEU cc_start: 0.8223 (mp) cc_final: 0.7925 (tt) REVERT: A 286 MET cc_start: 0.8163 (mtp) cc_final: 0.7846 (mtm) REVERT: A 345 MET cc_start: 0.8957 (ttp) cc_final: 0.8525 (ttp) REVERT: A 386 ARG cc_start: 0.7448 (tpt-90) cc_final: 0.6438 (tpp80) REVERT: B 219 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7289 (mmm-85) REVERT: B 548 LEU cc_start: 0.6853 (mp) cc_final: 0.6639 (mp) REVERT: B 569 MET cc_start: 0.7064 (mtp) cc_final: 0.6808 (mtp) outliers start: 27 outliers final: 15 residues processed: 116 average time/residue: 1.2344 time to fit residues: 151.8017 Evaluate side-chains 112 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 596 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 chunk 96 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.168937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128501 restraints weight = 9035.560| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.95 r_work: 0.3084 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8078 Z= 0.185 Angle : 0.612 8.440 10965 Z= 0.302 Chirality : 0.043 0.202 1243 Planarity : 0.005 0.058 1359 Dihedral : 4.412 30.955 1074 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.21 % Allowed : 22.45 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 2.18 (0.27), residues: 981 helix: 1.95 (0.19), residues: 697 sheet: None (None), residues: 0 loop : 0.27 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 26 HIS 0.004 0.001 HIS A 333 PHE 0.028 0.002 PHE B 310 TYR 0.011 0.002 TYR B 103 ARG 0.006 0.001 ARG B 265 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 529) hydrogen bonds : angle 4.30292 ( 1524) covalent geometry : bond 0.00451 ( 8078) covalent geometry : angle 0.61186 (10965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7408 (mmtt) cc_final: 0.6660 (tttm) REVERT: A 115 GLU cc_start: 0.6314 (mt-10) cc_final: 0.5735 (mp0) REVERT: A 181 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6111 (mm) REVERT: A 188 LYS cc_start: 0.5320 (mmtt) cc_final: 0.4823 (mppt) REVERT: A 234 LEU cc_start: 0.8340 (mp) cc_final: 0.8028 (tt) REVERT: A 345 MET cc_start: 0.9012 (ttp) cc_final: 0.8589 (ttp) REVERT: A 386 ARG cc_start: 0.7423 (tpt-90) cc_final: 0.6452 (tpp80) REVERT: A 463 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7524 (pp30) REVERT: B 219 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7418 (mmm-85) REVERT: B 548 LEU cc_start: 0.6978 (mp) cc_final: 0.6745 (mp) REVERT: B 569 MET cc_start: 0.7309 (mtp) cc_final: 0.7082 (mtp) outliers start: 27 outliers final: 16 residues processed: 116 average time/residue: 1.2789 time to fit residues: 157.2835 Evaluate side-chains 111 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 596 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.168188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126753 restraints weight = 8912.811| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.89 r_work: 0.3107 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8078 Z= 0.127 Angle : 0.550 9.149 10965 Z= 0.269 Chirality : 0.040 0.172 1243 Planarity : 0.004 0.057 1359 Dihedral : 4.312 31.967 1074 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.49 % Allowed : 23.63 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 2.44 (0.27), residues: 981 helix: 2.17 (0.20), residues: 695 sheet: None (None), residues: 0 loop : 0.34 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.003 0.001 HIS B 312 PHE 0.015 0.001 PHE B 298 TYR 0.008 0.001 TYR A 495 ARG 0.003 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 529) hydrogen bonds : angle 4.14125 ( 1524) covalent geometry : bond 0.00289 ( 8078) covalent geometry : angle 0.54999 (10965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7353 (mmtt) cc_final: 0.6622 (tttm) REVERT: A 35 ARG cc_start: 0.6348 (mmp-170) cc_final: 0.5914 (mtt90) REVERT: A 115 GLU cc_start: 0.6394 (mt-10) cc_final: 0.5787 (mp0) REVERT: A 181 ILE cc_start: 0.6548 (OUTLIER) cc_final: 0.5939 (mm) REVERT: A 188 LYS cc_start: 0.5299 (mmtt) cc_final: 0.4758 (mppt) REVERT: A 234 LEU cc_start: 0.8271 (mp) cc_final: 0.7964 (tt) REVERT: A 292 VAL cc_start: 0.7820 (t) cc_final: 0.7451 (p) REVERT: A 345 MET cc_start: 0.8982 (ttp) cc_final: 0.8564 (ttp) REVERT: A 386 ARG cc_start: 0.7409 (tpt-90) cc_final: 0.6440 (tpp80) REVERT: B 219 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7327 (mmm-85) REVERT: B 548 LEU cc_start: 0.6807 (mp) cc_final: 0.6594 (mp) outliers start: 21 outliers final: 15 residues processed: 113 average time/residue: 1.2580 time to fit residues: 150.7802 Evaluate side-chains 110 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 596 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 0.0170 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.173875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133094 restraints weight = 8869.282| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.89 r_work: 0.3154 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8078 Z= 0.111 Angle : 0.525 9.352 10965 Z= 0.258 Chirality : 0.039 0.172 1243 Planarity : 0.004 0.055 1359 Dihedral : 4.119 32.115 1074 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.66 % Allowed : 24.47 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 2.63 (0.27), residues: 981 helix: 2.26 (0.20), residues: 703 sheet: None (None), residues: 0 loop : 0.49 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 247 HIS 0.003 0.001 HIS B 312 PHE 0.030 0.001 PHE B 310 TYR 0.006 0.001 TYR A 495 ARG 0.002 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 529) hydrogen bonds : angle 4.01228 ( 1524) covalent geometry : bond 0.00236 ( 8078) covalent geometry : angle 0.52543 (10965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6421.38 seconds wall clock time: 109 minutes 50.34 seconds (6590.34 seconds total)