Starting phenix.real_space_refine on Wed Feb 12 12:21:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ten_41192/02_2025/8ten_41192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ten_41192/02_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_41192/02_2025/8ten_41192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ten_41192/02_2025/8ten_41192.map" model { file = "/net/cci-nas-00/data/ceres_data/8ten_41192/02_2025/8ten_41192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ten_41192/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.04, per 1000 atoms: 0.64 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: 1.86 Conformation dependent library (CDL) restraints added in 947.6 milliseconds 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: 0.80 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: 2.28 Time building geometry restraints manager: 2.16 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: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.570 Find NCS groups from input model: 0.140 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.700 ------------------------------------------------------------------------------- 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= 0.211 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 *********************** 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 : 0.777 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: 1.2870 time to fit residues: 143.1242 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 : 0.914 ------------------------------------------------------------------------------- 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: 0.3181 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- 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= 0.171 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 *********************** 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 : 0.920 Fit side-chains REVERT: A 23 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6553 (tttm) REVERT: A 234 LEU cc_start: 0.8218 (mp) cc_final: 0.7928 (tt) REVERT: A 345 MET cc_start: 0.8920 (ttp) cc_final: 0.8480 (ttp) REVERT: B 231 LEU cc_start: 0.6284 (tt) cc_final: 0.5999 (tt) REVERT: B 235 ILE cc_start: 0.7386 (mt) cc_final: 0.7017 (mt) REVERT: B 516 LEU cc_start: 0.7428 (tt) cc_final: 0.7202 (tp) REVERT: B 548 LEU cc_start: 0.6758 (mp) cc_final: 0.6497 (mt) outliers start: 29 outliers final: 12 residues processed: 122 average time/residue: 1.2249 time to fit residues: 159.1615 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 : 0.850 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.172049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130699 restraints weight = 8940.321| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.86 r_work: 0.3121 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1081 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= 0.199 Angle : 0.532 6.785 10965 Z= 0.265 Chirality : 0.040 0.158 1243 Planarity : 0.005 0.066 1359 Dihedral : 4.263 31.478 1075 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.16 % Allowed : 18.76 % Favored : 77.08 % 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: 2.13 (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 0.020 0.001 PHE B 310 TYR 0.009 0.001 TYR B 103 ARG 0.004 0.000 ARG A 150 *********************** 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 : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7429 (mmtt) cc_final: 0.6705 (tttm) REVERT: A 181 ILE cc_start: 0.6463 (OUTLIER) cc_final: 0.5971 (mm) REVERT: A 234 LEU cc_start: 0.8286 (mp) cc_final: 0.7998 (tt) REVERT: A 345 MET cc_start: 0.8972 (ttp) cc_final: 0.8542 (ttp) REVERT: B 228 THR cc_start: 0.4629 (OUTLIER) cc_final: 0.4388 (t) REVERT: B 463 GLN cc_start: 0.2829 (OUTLIER) cc_final: 0.2592 (mm110) REVERT: B 548 LEU cc_start: 0.6773 (mp) cc_final: 0.6482 (mt) REVERT: B 598 ASP cc_start: 0.4976 (t70) cc_final: 0.4737 (t70) outliers start: 35 outliers final: 15 residues processed: 125 average time/residue: 1.2193 time to fit residues: 161.8468 Evaluate side-chains 116 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 545 MET 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: 0.9980 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3901 r_free = 0.3901 target = 0.168773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127504 restraints weight = 8886.667| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.00 r_work: 0.3091 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8078 Z= 0.231 Angle : 0.560 7.038 10965 Z= 0.278 Chirality : 0.042 0.149 1243 Planarity : 0.005 0.062 1359 Dihedral : 4.395 31.655 1074 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.39 % Allowed : 19.36 % Favored : 76.25 % 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: 2.17 (0.27), residues: 981 helix: 1.96 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.22 (0.38), residues: 283 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 0.001 PHE B 30 TYR 0.010 0.001 TYR B 103 ARG 0.003 0.001 ARG B 265 *********************** 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: 37 poor density : 100 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7367 (mmtt) cc_final: 0.6623 (tttm) REVERT: A 181 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.5992 (mm) REVERT: A 183 GLU cc_start: 0.5300 (OUTLIER) cc_final: 0.5067 (mm-30) REVERT: A 188 LYS cc_start: 0.5188 (mmpt) cc_final: 0.4773 (mppt) REVERT: A 234 LEU cc_start: 0.8305 (mp) cc_final: 0.7980 (tt) REVERT: A 286 MET cc_start: 0.8130 (mtp) cc_final: 0.7891 (mtm) REVERT: A 345 MET cc_start: 0.9003 (ttp) cc_final: 0.8576 (ttp) REVERT: A 463 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7562 (pp30) REVERT: B 80 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5927 (ptt) REVERT: B 219 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7451 (mmm-85) REVERT: B 322 LYS cc_start: 0.3195 (OUTLIER) cc_final: 0.2987 (pttm) REVERT: B 523 ARG cc_start: 0.5567 (mmt90) cc_final: 0.5084 (mmt90) REVERT: B 548 LEU cc_start: 0.6919 (mp) cc_final: 0.6616 (mt) outliers start: 37 outliers final: 18 residues processed: 129 average time/residue: 1.2443 time to fit residues: 170.1633 Evaluate side-chains 122 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 80 MET 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 312 HIS Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 545 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: 3.9990 chunk 39 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.170552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129673 restraints weight = 8852.103| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.82 r_work: 0.3123 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1536 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= 0.193 Angle : 0.534 7.824 10965 Z= 0.263 Chirality : 0.040 0.142 1243 Planarity : 0.004 0.060 1359 Dihedral : 4.314 31.423 1074 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.92 % Allowed : 21.14 % Favored : 74.94 % 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: 2.36 (0.27), residues: 981 helix: 2.10 (0.20), residues: 693 sheet: None (None), residues: 0 loop : 0.33 (0.37), residues: 288 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 0.022 0.001 PHE B 310 TYR 0.008 0.001 TYR B 103 ARG 0.003 0.000 ARG B 523 *********************** 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 134 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7404 (mmtt) cc_final: 0.6686 (tttm) REVERT: A 35 ARG cc_start: 0.6380 (mmp-170) cc_final: 0.5957 (mtt90) REVERT: A 181 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6011 (mm) REVERT: A 188 LYS cc_start: 0.5270 (mmtt) cc_final: 0.4802 (mppt) REVERT: A 220 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8462 (mttp) REVERT: A 234 LEU cc_start: 0.8309 (mp) cc_final: 0.7987 (tt) REVERT: A 286 MET cc_start: 0.8117 (mtp) cc_final: 0.7839 (mtm) REVERT: A 345 MET cc_start: 0.8975 (ttp) cc_final: 0.8560 (ttp) REVERT: A 386 ARG cc_start: 0.7300 (tpt-90) cc_final: 0.6356 (tpp80) REVERT: A 452 ILE cc_start: 0.7298 (tp) cc_final: 0.7097 (tt) REVERT: A 463 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7397 (pp30) REVERT: B 219 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7425 (mmm-85) REVERT: B 228 THR cc_start: 0.4991 (OUTLIER) cc_final: 0.4676 (t) REVERT: B 522 ARG cc_start: 0.5835 (OUTLIER) cc_final: 0.5621 (tpt170) REVERT: B 548 LEU cc_start: 0.6858 (mp) cc_final: 0.6552 (mt) outliers start: 33 outliers final: 19 residues processed: 127 average time/residue: 1.2473 time to fit residues: 168.1759 Evaluate side-chains 121 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 122 LEU 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 345 MET Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 545 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: 0.5980 chunk 82 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.172148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130224 restraints weight = 8795.682| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.00 r_work: 0.3149 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1663 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= 0.157 Angle : 0.505 7.129 10965 Z= 0.248 Chirality : 0.039 0.142 1243 Planarity : 0.004 0.056 1359 Dihedral : 4.183 32.131 1074 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.92 % Allowed : 21.73 % 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: 2.57 (0.27), residues: 981 helix: 2.26 (0.20), residues: 693 sheet: None (None), residues: 0 loop : 0.42 (0.38), residues: 288 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 0.002 0.000 ARG A 118 *********************** 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 130 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7317 (mmtt) cc_final: 0.6614 (tttm) REVERT: A 35 ARG cc_start: 0.6364 (mmp-170) cc_final: 0.5899 (mtt90) REVERT: A 181 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.5851 (mm) REVERT: A 188 LYS cc_start: 0.5303 (mmtt) cc_final: 0.4769 (mppt) REVERT: A 220 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8420 (mttp) REVERT: A 234 LEU cc_start: 0.8252 (mp) cc_final: 0.7959 (tt) REVERT: A 286 MET cc_start: 0.8110 (mtp) cc_final: 0.7804 (mtm) REVERT: A 345 MET cc_start: 0.8949 (ttp) cc_final: 0.8531 (ttp) REVERT: A 386 ARG cc_start: 0.7339 (tpt-90) cc_final: 0.6321 (tpp80) REVERT: B 219 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7330 (mmm-85) REVERT: B 228 THR cc_start: 0.4955 (OUTLIER) cc_final: 0.4638 (t) REVERT: B 548 LEU cc_start: 0.6814 (mp) cc_final: 0.6501 (mt) outliers start: 33 outliers final: 16 residues processed: 123 average time/residue: 1.2986 time to fit residues: 169.0043 Evaluate side-chains 116 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 345 MET Chi-restraints excluded: chain B residue 545 MET 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: 5.9990 chunk 31 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.169245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127308 restraints weight = 8903.424| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.85 r_work: 0.3116 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8078 Z= 0.252 Angle : 0.581 7.305 10965 Z= 0.286 Chirality : 0.042 0.144 1243 Planarity : 0.005 0.058 1359 Dihedral : 4.408 30.921 1074 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.04 % Allowed : 21.97 % Favored : 73.99 % 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: 1.96 (0.19), residues: 695 sheet: None (None), residues: 0 loop : 0.25 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 247 HIS 0.004 0.001 HIS A 333 PHE 0.025 0.002 PHE B 310 TYR 0.011 0.001 TYR A 495 ARG 0.007 0.001 ARG B 18 *********************** 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 130 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7279 (mmtt) cc_final: 0.6535 (tttm) REVERT: A 181 ILE cc_start: 0.6585 (OUTLIER) cc_final: 0.5977 (mm) REVERT: A 188 LYS cc_start: 0.5273 (mmtt) cc_final: 0.4792 (mppt) REVERT: A 345 MET cc_start: 0.8956 (ttp) cc_final: 0.8543 (ttp) REVERT: A 386 ARG cc_start: 0.7322 (tpt-90) cc_final: 0.6283 (tpp80) REVERT: B 219 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7317 (mmm-85) REVERT: B 228 THR cc_start: 0.5070 (OUTLIER) cc_final: 0.4732 (t) REVERT: B 548 LEU cc_start: 0.6735 (mp) cc_final: 0.6517 (mp) REVERT: B 569 MET cc_start: 0.7213 (mtp) cc_final: 0.6956 (mtp) outliers start: 34 outliers final: 18 residues processed: 123 average time/residue: 1.2484 time to fit residues: 163.0655 Evaluate side-chains 114 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 228 THR Chi-restraints excluded: chain A residue 257 ASP 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 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 345 MET Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 561 THR 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: 0.9980 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.171407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129701 restraints weight = 8912.260| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.77 r_work: 0.3153 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8078 Z= 0.160 Angle : 0.523 8.023 10965 Z= 0.256 Chirality : 0.039 0.160 1243 Planarity : 0.004 0.056 1359 Dihedral : 4.237 32.318 1074 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.09 % Allowed : 23.40 % Favored : 73.52 % 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: 2.54 (0.27), residues: 981 helix: 2.23 (0.20), residues: 695 sheet: None (None), residues: 0 loop : 0.41 (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 0.012 0.001 PHE B 298 TYR 0.007 0.001 TYR A 495 ARG 0.004 0.000 ARG B 18 *********************** 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 118 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7367 (mmtt) cc_final: 0.6654 (tttm) REVERT: A 35 ARG cc_start: 0.6356 (mmp-170) cc_final: 0.5927 (mtt90) REVERT: A 181 ILE cc_start: 0.6510 (OUTLIER) cc_final: 0.5905 (mm) REVERT: A 188 LYS cc_start: 0.5279 (mmtt) cc_final: 0.4739 (mppt) REVERT: A 234 LEU cc_start: 0.8261 (mp) cc_final: 0.7959 (tt) REVERT: A 292 VAL cc_start: 0.7755 (t) cc_final: 0.7402 (p) REVERT: A 345 MET cc_start: 0.8955 (ttp) cc_final: 0.8527 (ttp) REVERT: A 386 ARG cc_start: 0.7343 (tpt-90) cc_final: 0.6332 (tpp80) REVERT: B 111 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7599 (ttmm) REVERT: B 219 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7340 (mmm-85) REVERT: B 228 THR cc_start: 0.5140 (OUTLIER) cc_final: 0.4832 (t) REVERT: B 303 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.7002 (mpp) REVERT: B 548 LEU cc_start: 0.6853 (mp) cc_final: 0.6637 (mp) outliers start: 26 outliers final: 17 residues processed: 113 average time/residue: 1.2690 time to fit residues: 152.2066 Evaluate side-chains 116 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 20 MET 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 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 111 LYS Chi-restraints excluded: chain B residue 122 LEU 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 303 MET Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 545 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: 2.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.167836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128242 restraints weight = 9056.137| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.82 r_work: 0.3121 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8078 Z= 0.244 Angle : 0.580 8.551 10965 Z= 0.285 Chirality : 0.042 0.160 1243 Planarity : 0.005 0.057 1359 Dihedral : 4.389 31.326 1074 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.68 % Allowed : 22.57 % Favored : 73.75 % 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: 2.25 (0.27), residues: 981 helix: 2.01 (0.20), residues: 696 sheet: None (None), residues: 0 loop : 0.29 (0.38), residues: 285 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 0.024 0.001 PHE B 310 TYR 0.009 0.001 TYR A 495 ARG 0.004 0.001 ARG B 18 *********************** 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 126 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7393 (mmtt) cc_final: 0.6635 (tttm) REVERT: A 35 ARG cc_start: 0.6454 (mmp-170) cc_final: 0.5989 (mtt90) REVERT: A 115 GLU cc_start: 0.6401 (mt-10) cc_final: 0.5756 (mp0) REVERT: A 181 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6069 (mm) REVERT: A 188 LYS cc_start: 0.5304 (mmtt) cc_final: 0.4783 (mppt) REVERT: A 234 LEU cc_start: 0.8278 (mp) cc_final: 0.7928 (tt) REVERT: A 345 MET cc_start: 0.8967 (ttp) cc_final: 0.8547 (ttp) REVERT: A 386 ARG cc_start: 0.7334 (tpt-90) cc_final: 0.6294 (tpp80) REVERT: B 111 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7628 (ttmm) REVERT: B 219 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7352 (mmm-85) REVERT: B 228 THR cc_start: 0.5015 (OUTLIER) cc_final: 0.4712 (t) REVERT: B 548 LEU cc_start: 0.6858 (mp) cc_final: 0.6623 (mp) outliers start: 31 outliers final: 20 residues processed: 119 average time/residue: 1.3418 time to fit residues: 168.5911 Evaluate side-chains 118 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 20 MET 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 502 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 122 LEU 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 345 MET Chi-restraints excluded: chain B residue 545 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: 1.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.170825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129443 restraints weight = 8872.393| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.85 r_work: 0.3120 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8078 Z= 0.169 Angle : 0.541 9.318 10965 Z= 0.265 Chirality : 0.040 0.162 1243 Planarity : 0.004 0.056 1359 Dihedral : 4.286 32.262 1074 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.38 % Allowed : 24.35 % Favored : 73.28 % 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: 2.49 (0.27), residues: 981 helix: 2.19 (0.20), residues: 695 sheet: None (None), residues: 0 loop : 0.39 (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 0.013 0.001 PHE B 298 TYR 0.008 0.001 TYR A 495 ARG 0.003 0.000 ARG B 18 ********************** 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 115 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7383 (mmtt) cc_final: 0.6651 (tttm) REVERT: A 35 ARG cc_start: 0.6407 (mmp-170) cc_final: 0.5940 (mtt90) REVERT: A 115 GLU cc_start: 0.6427 (mt-10) cc_final: 0.5810 (mp0) REVERT: A 181 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.5990 (mm) REVERT: A 188 LYS cc_start: 0.5344 (mmtt) cc_final: 0.4797 (mppt) REVERT: A 234 LEU cc_start: 0.8275 (mp) cc_final: 0.7967 (tt) REVERT: A 292 VAL cc_start: 0.7800 (t) cc_final: 0.7431 (p) REVERT: A 345 MET cc_start: 0.8968 (ttp) cc_final: 0.8537 (ttp) REVERT: A 386 ARG cc_start: 0.7349 (tpt-90) cc_final: 0.6354 (tpp80) REVERT: B 111 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7661 (ttmm) REVERT: B 219 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7348 (mmm-85) REVERT: B 228 THR cc_start: 0.5058 (OUTLIER) cc_final: 0.4742 (t) REVERT: B 548 LEU cc_start: 0.6887 (mp) cc_final: 0.6655 (mp) outliers start: 20 outliers final: 16 residues processed: 111 average time/residue: 1.3250 time to fit residues: 155.5332 Evaluate side-chains 115 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS 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 502 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 122 LEU 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 303 MET Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 545 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: 1.9990 chunk 13 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 0.0470 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 47 optimal weight: 2.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.173411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132518 restraints weight = 8827.131| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.91 r_work: 0.3164 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8078 Z= 0.152 Angle : 0.524 9.346 10965 Z= 0.256 Chirality : 0.039 0.163 1243 Planarity : 0.004 0.053 1359 Dihedral : 4.127 31.976 1074 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.73 % Allowed : 24.23 % Favored : 73.04 % 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: 2.58 (0.27), residues: 981 helix: 2.22 (0.20), residues: 703 sheet: None (None), residues: 0 loop : 0.48 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 247 HIS 0.004 0.001 HIS B 531 PHE 0.029 0.001 PHE B 310 TYR 0.009 0.001 TYR B 495 ARG 0.003 0.000 ARG A 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6103.64 seconds wall clock time: 108 minutes 9.53 seconds (6489.53 seconds total)