Starting phenix.real_space_refine on Wed Feb 12 21:13:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fti_29433/02_2025/8fti_29433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fti_29433/02_2025/8fti_29433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fti_29433/02_2025/8fti_29433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fti_29433/02_2025/8fti_29433.map" model { file = "/net/cci-nas-00/data/ceres_data/8fti_29433/02_2025/8fti_29433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fti_29433/02_2025/8fti_29433.cif" } resolution = 3.5 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= 0.020 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 97 5.49 5 S 24 5.16 5 C 4792 2.51 5 N 1443 2.21 5 O 1770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8126 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 6062 Classifications: {'peptide': 737} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 725} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2064 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 45, 'rna3p_pyr': 38} Link IDs: {'rna2p': 13, 'rna3p': 83} Chain breaks: 1 Time building chain proxies: 5.45, per 1000 atoms: 0.67 Number of scatterers: 8126 At special positions: 0 Unit cell: (77.43, 81.78, 137.46, 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 24 16.00 P 97 15.00 O 1770 8.00 N 1443 7.00 C 4792 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: 2.09 Conformation dependent library (CDL) restraints added in 658.3 milliseconds 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 61.9% alpha, 3.7% beta 33 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.639A pdb=" N ARG A 23 " --> pdb=" O GLN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 41 removed outlier: 3.980A pdb=" N ILE A 29 " --> pdb=" O TRP A 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 30 " --> pdb=" O CYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 62 through 72 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.641A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 123 removed outlier: 3.509A pdb=" N THR A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 151 removed outlier: 4.133A pdb=" N PHE A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.676A pdb=" N LYS A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.616A pdb=" N ASP A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.751A pdb=" N TYR A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.707A pdb=" N PHE A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.624A pdb=" N TYR A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 360 removed outlier: 3.652A pdb=" N ALA A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLN A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.741A pdb=" N LEU A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 408 Processing helix chain 'A' and resid 413 through 429 removed outlier: 3.777A pdb=" N TYR A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 447 removed outlier: 3.992A pdb=" N ASN A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.624A pdb=" N PHE A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.844A pdb=" N TYR A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 497 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.691A pdb=" N LYS A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.723A pdb=" N LYS A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.592A pdb=" N HIS A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 606 removed outlier: 3.758A pdb=" N LEU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 591 " --> pdb=" O TYR A 587 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 652 through 662 removed outlier: 3.628A pdb=" N GLY A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 706 removed outlier: 3.970A pdb=" N PHE A 680 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG A 681 " --> pdb=" O GLU A 677 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 744 Processing helix chain 'A' and resid 750 through 764 removed outlier: 4.374A pdb=" N PHE A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 755 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 764 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 291 removed outlier: 3.831A pdb=" N VAL A 289 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 267 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 300 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 307 through 314 removed outlier: 4.226A pdb=" N LYS A 314 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 317 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 616 through 618 290 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1843 1.33 - 1.45: 2318 1.45 - 1.57: 4105 1.57 - 1.69: 192 1.69 - 1.81: 34 Bond restraints: 8492 Sorted by residual: bond pdb=" C TRP A 770 " pdb=" N LYS A 771 " ideal model delta sigma weight residual 1.328 1.339 -0.011 1.30e-02 5.92e+03 6.93e-01 bond pdb=" CA GLN A 74 " pdb=" CB GLN A 74 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.55e-01 bond pdb=" N LYS A 771 " pdb=" CA LYS A 771 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.42e-02 4.96e+03 6.01e-01 bond pdb=" C LEU A 649 " pdb=" N ASP A 650 " ideal model delta sigma weight residual 1.327 1.334 -0.007 9.40e-03 1.13e+04 5.85e-01 bond pdb=" N ASN A 238 " pdb=" CA ASN A 238 " ideal model delta sigma weight residual 1.463 1.456 0.008 1.08e-02 8.57e+03 5.11e-01 ... (remaining 8487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 11509 1.37 - 2.75: 308 2.75 - 4.12: 56 4.12 - 5.50: 11 5.50 - 6.87: 1 Bond angle restraints: 11885 Sorted by residual: angle pdb=" C THR A 73 " pdb=" N GLN A 74 " pdb=" CA GLN A 74 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C ALA A 463 " pdb=" N GLU A 464 " pdb=" CA GLU A 464 " ideal model delta sigma weight residual 122.74 126.45 -3.71 1.44e+00 4.82e-01 6.65e+00 angle pdb=" N ASN A 583 " pdb=" CA ASN A 583 " pdb=" C ASN A 583 " ideal model delta sigma weight residual 109.81 114.81 -5.00 2.21e+00 2.05e-01 5.11e+00 angle pdb=" CA ASN A 583 " pdb=" C ASN A 583 " pdb=" N PRO A 584 " ideal model delta sigma weight residual 118.44 121.89 -3.45 1.59e+00 3.96e-01 4.72e+00 angle pdb=" C PRO A 773 " pdb=" N VAL A 774 " pdb=" CA VAL A 774 " ideal model delta sigma weight residual 121.97 125.86 -3.89 1.80e+00 3.09e-01 4.66e+00 ... (remaining 11880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 4895 34.54 - 69.07: 289 69.07 - 103.61: 24 103.61 - 138.15: 0 138.15 - 172.68: 1 Dihedral angle restraints: 5209 sinusoidal: 3059 harmonic: 2150 Sorted by residual: dihedral pdb=" CA GLY A 644 " pdb=" C GLY A 644 " pdb=" N LYS A 645 " pdb=" CA LYS A 645 " ideal model delta harmonic sigma weight residual -180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" C4' C B -1 " pdb=" C3' C B -1 " pdb=" O3' C B -1 " pdb=" P G B 0 " ideal model delta sinusoidal sigma weight residual -140.00 32.68 -172.68 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ARG A 349 " pdb=" C ARG A 349 " pdb=" N TYR A 350 " pdb=" CA TYR A 350 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 979 0.028 - 0.056: 264 0.056 - 0.083: 66 0.083 - 0.111: 34 0.111 - 0.139: 11 Chirality restraints: 1354 Sorted by residual: chirality pdb=" C1' A B -24 " pdb=" O4' A B -24 " pdb=" C2' A B -24 " pdb=" N9 A B -24 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE A 636 " pdb=" N ILE A 636 " pdb=" C ILE A 636 " pdb=" CB ILE A 636 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1351 not shown) Planarity restraints: 1162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 583 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 584 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 584 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 584 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 4 " 0.018 2.00e-02 2.50e+03 9.03e-03 2.44e+00 pdb=" N9 G B 4 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B 4 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 4 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B 4 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 4 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B -24 " -0.019 2.00e-02 2.50e+03 8.87e-03 2.16e+00 pdb=" N9 A B -24 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A B -24 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B -24 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A B -24 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B -24 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A B -24 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A B -24 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B -24 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B -24 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A B -24 " -0.000 2.00e-02 2.50e+03 ... (remaining 1159 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1653 2.77 - 3.30: 7856 3.30 - 3.83: 13459 3.83 - 4.37: 15275 4.37 - 4.90: 23661 Nonbonded interactions: 61904 Sorted by model distance: nonbonded pdb=" OH TYR A 253 " pdb=" OG SER A 335 " model vdw 2.237 3.040 nonbonded pdb=" OE1 GLN A 257 " pdb=" OH TYR A 602 " model vdw 2.250 3.040 nonbonded pdb=" O GLU A 104 " pdb=" OG1 THR A 107 " model vdw 2.255 3.040 nonbonded pdb=" O PHE A 147 " pdb=" OG SER A 150 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLU A 552 " pdb=" NE ARG A 594 " model vdw 2.303 3.120 ... (remaining 61899 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.460 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 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 : 0.002 0.026 8492 Z= 0.157 Angle : 0.559 6.869 11885 Z= 0.323 Chirality : 0.032 0.139 1354 Planarity : 0.003 0.047 1162 Dihedral : 18.080 172.685 3829 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.55 % Allowed : 10.34 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.31), residues: 729 helix: 1.10 (0.25), residues: 419 sheet: -0.24 (1.17), residues: 27 loop : -1.24 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 402 HIS 0.003 0.001 HIS A 554 PHE 0.017 0.001 PHE A 638 TYR 0.013 0.001 TYR A 321 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5421 (mtt-85) REVERT: A 518 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7689 (mmmt) REVERT: A 761 MET cc_start: 0.7806 (tpt) cc_final: 0.7345 (tpp) REVERT: A 770 TRP cc_start: 0.5377 (OUTLIER) cc_final: 0.3557 (m-90) outliers start: 29 outliers final: 12 residues processed: 112 average time/residue: 0.2723 time to fit residues: 38.8643 Evaluate side-chains 73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 770 TRP Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 64 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 476 GLN A 561 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.162156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.122065 restraints weight = 15520.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.126035 restraints weight = 8499.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.128548 restraints weight = 5983.124| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8492 Z= 0.146 Angle : 0.530 5.791 11885 Z= 0.282 Chirality : 0.034 0.143 1354 Planarity : 0.003 0.042 1162 Dihedral : 19.234 162.858 2353 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.76 % Allowed : 14.89 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.31), residues: 729 helix: 1.56 (0.25), residues: 429 sheet: -0.18 (1.14), residues: 29 loop : -1.31 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.003 0.000 HIS A 673 PHE 0.018 0.001 PHE A 638 TYR 0.011 0.001 TYR A 321 ARG 0.004 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 191 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.4841 (mtt-85) REVERT: A 334 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7949 (tt) REVERT: A 608 ARG cc_start: 0.5569 (tpt-90) cc_final: 0.5365 (ttt-90) REVERT: A 657 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7533 (tpp80) REVERT: A 663 MET cc_start: 0.6947 (tpt) cc_final: 0.6626 (tpt) REVERT: A 770 TRP cc_start: 0.5450 (OUTLIER) cc_final: 0.3453 (m-90) outliers start: 24 outliers final: 18 residues processed: 90 average time/residue: 0.2355 time to fit residues: 28.2916 Evaluate side-chains 81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 770 TRP Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.160491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.123706 restraints weight = 15484.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.126600 restraints weight = 9146.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.128081 restraints weight = 5873.547| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8492 Z= 0.165 Angle : 0.522 6.179 11885 Z= 0.276 Chirality : 0.034 0.164 1354 Planarity : 0.003 0.041 1162 Dihedral : 19.163 162.913 2347 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.39 % Allowed : 15.83 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.31), residues: 729 helix: 1.76 (0.25), residues: 423 sheet: -0.27 (1.12), residues: 29 loop : -1.49 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.004 0.001 HIS A 554 PHE 0.021 0.001 PHE A 638 TYR 0.013 0.001 TYR A 321 ARG 0.003 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 61 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: A 110 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 191 ARG cc_start: 0.6176 (OUTLIER) cc_final: 0.4611 (mtt-85) REVERT: A 334 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7954 (tt) REVERT: A 518 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6975 (mmmt) REVERT: A 657 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7394 (tpp80) REVERT: A 698 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 770 TRP cc_start: 0.5521 (OUTLIER) cc_final: 0.3544 (m-90) outliers start: 28 outliers final: 18 residues processed: 88 average time/residue: 0.2460 time to fit residues: 28.7253 Evaluate side-chains 79 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 770 TRP Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.155864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.114956 restraints weight = 15772.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118689 restraints weight = 8939.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.120984 restraints weight = 6410.658| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8492 Z= 0.251 Angle : 0.602 10.510 11885 Z= 0.315 Chirality : 0.037 0.192 1354 Planarity : 0.004 0.046 1162 Dihedral : 19.238 163.876 2341 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 6.11 % Allowed : 16.30 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.30), residues: 729 helix: 1.48 (0.25), residues: 420 sheet: -0.52 (1.04), residues: 31 loop : -1.64 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 402 HIS 0.005 0.001 HIS A 415 PHE 0.022 0.002 PHE A 638 TYR 0.018 0.002 TYR A 321 ARG 0.002 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 60 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7930 (ttt180) REVERT: A 191 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.4812 (mtt-85) REVERT: A 247 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7778 (mt) REVERT: A 334 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8074 (tt) REVERT: A 518 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6960 (mmmt) REVERT: A 608 ARG cc_start: 0.5418 (tpt-90) cc_final: 0.5003 (tpt-90) REVERT: A 657 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7468 (tpp80) REVERT: A 663 MET cc_start: 0.7381 (tpt) cc_final: 0.7181 (tpt) REVERT: A 770 TRP cc_start: 0.5626 (OUTLIER) cc_final: 0.3440 (m-90) outliers start: 39 outliers final: 26 residues processed: 95 average time/residue: 0.2416 time to fit residues: 30.3177 Evaluate side-chains 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 770 TRP Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.154758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.113638 restraints weight = 15271.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.117234 restraints weight = 8675.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.119473 restraints weight = 6236.660| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8492 Z= 0.325 Angle : 0.666 8.465 11885 Z= 0.349 Chirality : 0.040 0.258 1354 Planarity : 0.004 0.051 1162 Dihedral : 19.370 165.373 2339 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.80 % Allowed : 17.55 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 729 helix: 1.20 (0.25), residues: 419 sheet: -0.56 (1.06), residues: 31 loop : -1.87 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 60 HIS 0.006 0.001 HIS A 415 PHE 0.025 0.002 PHE A 638 TYR 0.021 0.002 TYR A 321 ARG 0.003 0.001 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 55 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7932 (ttt-90) REVERT: A 191 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5320 (mtt-85) REVERT: A 247 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7750 (mt) REVERT: A 334 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8129 (tt) REVERT: A 518 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6855 (mmmt) REVERT: A 770 TRP cc_start: 0.5538 (OUTLIER) cc_final: 0.3359 (m-90) outliers start: 37 outliers final: 27 residues processed: 91 average time/residue: 0.2555 time to fit residues: 31.0674 Evaluate side-chains 86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 770 TRP Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 21 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.155903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.115244 restraints weight = 15452.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.118894 restraints weight = 8881.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.121141 restraints weight = 6396.732| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8492 Z= 0.220 Angle : 0.580 7.509 11885 Z= 0.307 Chirality : 0.037 0.210 1354 Planarity : 0.004 0.052 1162 Dihedral : 19.181 163.891 2338 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.49 % Allowed : 18.97 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.30), residues: 729 helix: 1.38 (0.25), residues: 419 sheet: -0.55 (1.05), residues: 31 loop : -1.83 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 402 HIS 0.004 0.001 HIS A 415 PHE 0.023 0.002 PHE A 638 TYR 0.023 0.001 TYR A 175 ARG 0.003 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5023 (mtt-85) REVERT: A 247 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7806 (mt) REVERT: A 334 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8010 (tt) REVERT: A 392 ASP cc_start: 0.7790 (p0) cc_final: 0.7583 (p0) REVERT: A 518 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6962 (mmmt) REVERT: A 663 MET cc_start: 0.7222 (tpt) cc_final: 0.6594 (tpp) REVERT: A 770 TRP cc_start: 0.5701 (OUTLIER) cc_final: 0.3509 (m-90) outliers start: 35 outliers final: 25 residues processed: 92 average time/residue: 0.2387 time to fit residues: 29.2961 Evaluate side-chains 87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 770 TRP Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.159613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.119254 restraints weight = 15532.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.123081 restraints weight = 8702.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.125487 restraints weight = 6192.450| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8492 Z= 0.149 Angle : 0.524 7.281 11885 Z= 0.279 Chirality : 0.035 0.156 1354 Planarity : 0.003 0.049 1162 Dihedral : 18.918 162.261 2338 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.94 % Favored : 94.92 % Rotamer: Outliers : 3.76 % Allowed : 20.69 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 729 helix: 1.64 (0.25), residues: 422 sheet: -0.35 (1.11), residues: 29 loop : -1.76 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 402 HIS 0.005 0.001 HIS A 665 PHE 0.017 0.001 PHE A 638 TYR 0.023 0.001 TYR A 471 ARG 0.003 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 191 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.4895 (mtt-85) REVERT: A 334 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7930 (tt) REVERT: A 740 ARG cc_start: 0.7850 (ptt90) cc_final: 0.7369 (mmp-170) outliers start: 24 outliers final: 16 residues processed: 87 average time/residue: 0.2190 time to fit residues: 26.0307 Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.154395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.113460 restraints weight = 15659.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.116924 restraints weight = 9162.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119079 restraints weight = 6682.423| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8492 Z= 0.314 Angle : 0.651 8.616 11885 Z= 0.341 Chirality : 0.040 0.219 1354 Planarity : 0.004 0.056 1162 Dihedral : 19.160 164.550 2335 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.86 % Allowed : 20.38 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.30), residues: 729 helix: 1.27 (0.25), residues: 419 sheet: -0.63 (1.04), residues: 31 loop : -1.88 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 60 HIS 0.005 0.001 HIS A 415 PHE 0.025 0.002 PHE A 638 TYR 0.025 0.002 TYR A 175 ARG 0.005 0.001 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 191 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5140 (mtt-85) REVERT: A 247 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7835 (mt) REVERT: A 334 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8131 (tt) REVERT: A 458 LYS cc_start: 0.8694 (tppt) cc_final: 0.8440 (pttm) REVERT: A 518 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6977 (mmmt) REVERT: A 573 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5991 (tt) outliers start: 31 outliers final: 22 residues processed: 84 average time/residue: 0.2301 time to fit residues: 25.8603 Evaluate side-chains 81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.159950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.123704 restraints weight = 15845.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.126167 restraints weight = 9374.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.126988 restraints weight = 6342.127| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8492 Z= 0.147 Angle : 0.548 9.675 11885 Z= 0.289 Chirality : 0.035 0.159 1354 Planarity : 0.003 0.048 1162 Dihedral : 18.866 162.414 2335 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.92 % Allowed : 21.32 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.31), residues: 729 helix: 1.65 (0.25), residues: 422 sheet: -0.38 (1.11), residues: 29 loop : -1.81 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 402 HIS 0.003 0.001 HIS A 52 PHE 0.018 0.001 PHE A 638 TYR 0.011 0.001 TYR A 61 ARG 0.004 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7948 (tm-30) REVERT: A 191 ARG cc_start: 0.6031 (OUTLIER) cc_final: 0.4973 (mtt-85) REVERT: A 334 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7915 (tt) REVERT: A 657 ARG cc_start: 0.7926 (tpp80) cc_final: 0.7513 (tpp80) REVERT: A 740 ARG cc_start: 0.7738 (ptt90) cc_final: 0.7376 (mmp-170) outliers start: 25 outliers final: 20 residues processed: 89 average time/residue: 0.2396 time to fit residues: 28.4299 Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 0.3980 chunk 50 optimal weight: 0.0980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.156895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.115907 restraints weight = 15688.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.119670 restraints weight = 8780.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122027 restraints weight = 6251.962| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8492 Z= 0.237 Angle : 0.596 8.471 11885 Z= 0.312 Chirality : 0.037 0.196 1354 Planarity : 0.004 0.050 1162 Dihedral : 18.970 163.172 2335 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.61 % Allowed : 21.47 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.31), residues: 729 helix: 1.54 (0.25), residues: 419 sheet: -0.51 (1.04), residues: 31 loop : -1.85 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.004 0.001 HIS A 554 PHE 0.024 0.002 PHE A 638 TYR 0.027 0.002 TYR A 175 ARG 0.003 0.000 ARG A 740 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7985 (tm-30) REVERT: A 191 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.4982 (mtt-85) REVERT: A 334 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8042 (tt) REVERT: A 518 LYS cc_start: 0.7321 (mmmt) cc_final: 0.7051 (tptp) REVERT: A 657 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7480 (tpp80) REVERT: A 740 ARG cc_start: 0.7844 (ptt90) cc_final: 0.7454 (mmp-170) outliers start: 23 outliers final: 19 residues processed: 86 average time/residue: 0.2526 time to fit residues: 28.7128 Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4244 r_free = 0.4244 target = 0.156689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.115972 restraints weight = 15958.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119566 restraints weight = 9246.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.121775 restraints weight = 6719.656| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8492 Z= 0.243 Angle : 0.606 8.182 11885 Z= 0.318 Chirality : 0.037 0.192 1354 Planarity : 0.004 0.050 1162 Dihedral : 18.989 163.362 2335 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.23 % Allowed : 21.00 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.31), residues: 729 helix: 1.42 (0.25), residues: 419 sheet: -0.55 (1.04), residues: 31 loop : -1.83 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.004 0.001 HIS A 554 PHE 0.023 0.002 PHE A 638 TYR 0.015 0.001 TYR A 321 ARG 0.004 0.000 ARG A 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2673.56 seconds wall clock time: 48 minutes 39.02 seconds (2919.02 seconds total)