Starting phenix.real_space_refine on Sun May 11 02:18:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9inf_60705/05_2025/9inf_60705.cif Found real_map, /net/cci-nas-00/data/ceres_data/9inf_60705/05_2025/9inf_60705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9inf_60705/05_2025/9inf_60705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9inf_60705/05_2025/9inf_60705.map" model { file = "/net/cci-nas-00/data/ceres_data/9inf_60705/05_2025/9inf_60705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9inf_60705/05_2025/9inf_60705.cif" } resolution = 3.36 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= 0.013 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 6 5.49 5 S 32 5.16 5 C 5000 2.51 5 N 1076 2.21 5 O 1168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7282 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3333 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 385} Chain: "B" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3333 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 385} Chain: "A" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 333 Unusual residues: {'3PE': 3, 'ACD': 1, 'CLR': 5, 'PLM': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 277 Unusual residues: {'3PE': 3, 'ACD': 1, 'CLR': 3, 'PLM': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 8.01, per 1000 atoms: 1.10 Number of scatterers: 7282 At special positions: 0 Unit cell: (107.551, 96.057, 75.532, 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 32 16.00 P 6 15.00 O 1168 8.00 N 1076 7.00 C 5000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 841.6 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1524 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.207A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.531A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 removed outlier: 4.240A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 removed outlier: 3.583A pdb=" N HIS A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.851A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 503 removed outlier: 4.135A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 Processing helix chain 'A' and resid 538 through 542 removed outlier: 4.383A pdb=" N GLY A 542 " --> pdb=" O LYS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 580 removed outlier: 3.862A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 618 removed outlier: 4.247A pdb=" N ASP A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Proline residue: A 598 - end of helix Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.133A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 312 through 336 Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 removed outlier: 3.853A pdb=" N HIS B 387 " --> pdb=" O ALA B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.753A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 471 Proline residue: B 455 - end of helix removed outlier: 3.622A pdb=" N ARG B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 502 removed outlier: 4.202A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 506 through 532 Processing helix chain 'B' and resid 538 through 542 removed outlier: 4.408A pdb=" N GLY B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 581 removed outlier: 3.888A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 618 removed outlier: 4.103A pdb=" N ASP B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.654A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1377 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: 2.01 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1099 1.33 - 1.45: 2156 1.45 - 1.57: 4201 1.57 - 1.69: 12 1.69 - 1.82: 44 Bond restraints: 7512 Sorted by residual: bond pdb=" CA THR A 491 " pdb=" C THR A 491 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.24e-02 6.50e+03 5.02e+00 bond pdb=" C1 PLM B 807 " pdb=" C2 PLM B 807 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" CG LEU B 421 " pdb=" CD1 LEU B 421 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.76e+00 bond pdb=" CA LEU A 419 " pdb=" C LEU A 419 " ideal model delta sigma weight residual 1.519 1.533 -0.013 1.01e-02 9.80e+03 1.71e+00 bond pdb=" C1 PLM A 809 " pdb=" C2 PLM A 809 " ideal model delta sigma weight residual 1.542 1.568 -0.026 2.00e-02 2.50e+03 1.67e+00 ... (remaining 7507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 9942 1.87 - 3.73: 169 3.73 - 5.60: 38 5.60 - 7.46: 12 7.46 - 9.33: 5 Bond angle restraints: 10166 Sorted by residual: angle pdb=" C THR A 491 " pdb=" CA THR A 491 " pdb=" CB THR A 491 " ideal model delta sigma weight residual 110.96 105.38 5.58 1.54e+00 4.22e-01 1.31e+01 angle pdb=" C THR A 383 " pdb=" N ALA A 384 " pdb=" CA ALA A 384 " ideal model delta sigma weight residual 120.26 124.36 -4.10 1.34e+00 5.57e-01 9.35e+00 angle pdb=" N THR A 491 " pdb=" CA THR A 491 " pdb=" C THR A 491 " ideal model delta sigma weight residual 110.97 107.84 3.13 1.09e+00 8.42e-01 8.26e+00 angle pdb=" N THR A 491 " pdb=" CA THR A 491 " pdb=" CB THR A 491 " ideal model delta sigma weight residual 109.91 114.05 -4.14 1.46e+00 4.69e-01 8.03e+00 angle pdb=" C SER B 418 " pdb=" N LEU B 419 " pdb=" CA LEU B 419 " ideal model delta sigma weight residual 122.46 117.50 4.96 1.80e+00 3.09e-01 7.61e+00 ... (remaining 10161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 4226 22.87 - 45.75: 457 45.75 - 68.62: 88 68.62 - 91.50: 5 91.50 - 114.37: 8 Dihedral angle restraints: 4784 sinusoidal: 2418 harmonic: 2366 Sorted by residual: dihedral pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " pdb=" CB CYS B 440 " ideal model delta sinusoidal sigma weight residual 93.00 172.38 -79.38 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS A 415 " pdb=" SG CYS A 415 " pdb=" SG CYS A 440 " pdb=" CB CYS A 440 " ideal model delta sinusoidal sigma weight residual 93.00 164.66 -71.66 1 1.00e+01 1.00e-02 6.58e+01 dihedral pdb=" CA LEU B 419 " pdb=" C LEU B 419 " pdb=" N GLU B 420 " pdb=" CA GLU B 420 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1015 0.076 - 0.153: 73 0.153 - 0.229: 4 0.229 - 0.306: 1 0.306 - 0.382: 1 Chirality restraints: 1094 Sorted by residual: chirality pdb=" C17 CLR A 807 " pdb=" C13 CLR A 807 " pdb=" C16 CLR A 807 " pdb=" C20 CLR A 807 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C20 CLR A 807 " pdb=" C17 CLR A 807 " pdb=" C21 CLR A 807 " pdb=" C22 CLR A 807 " both_signs ideal model delta sigma weight residual False 2.59 2.35 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU A 396 " pdb=" CB LEU A 396 " pdb=" CD1 LEU A 396 " pdb=" CD2 LEU A 396 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1091 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 573 " 0.013 2.00e-02 2.50e+03 1.64e-02 6.70e+00 pdb=" CG TRP A 573 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 573 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 573 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 573 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 573 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 573 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 573 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 573 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 573 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 514 " -0.017 2.00e-02 2.50e+03 1.54e-02 5.93e+00 pdb=" CG TRP B 514 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 514 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 514 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 514 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 514 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 514 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 514 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 514 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 514 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 528 " 0.018 2.00e-02 2.50e+03 1.42e-02 5.05e+00 pdb=" CG TRP A 528 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 528 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 528 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 528 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 528 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 528 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 528 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 528 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 528 " 0.006 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 777 2.75 - 3.29: 7498 3.29 - 3.82: 12803 3.82 - 4.36: 14733 4.36 - 4.90: 24980 Nonbonded interactions: 60791 Sorted by model distance: nonbonded pdb=" OH TYR A 559 " pdb=" OE2 GLU A 613 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP A 529 " pdb=" NH2 ARG A 570 " model vdw 2.215 3.120 nonbonded pdb=" O SER B 578 " pdb=" OG1 THR B 583 " model vdw 2.220 3.040 nonbonded pdb=" O ILE B 271 " pdb=" OH TYR B 352 " model vdw 2.246 3.040 nonbonded pdb=" O ILE A 271 " pdb=" OH TYR A 352 " model vdw 2.258 3.040 ... (remaining 60786 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 226 through 626 or resid 801 through 804)) selection = (chain 'B' and (resid 226 through 626 or resid 801 through 804)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 11.560 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.130 Process input model: 26.270 Find NCS groups from input model: 0.310 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 0.045 7514 Z= 0.148 Angle : 0.675 9.330 10170 Z= 0.348 Chirality : 0.043 0.382 1094 Planarity : 0.004 0.053 1172 Dihedral : 17.898 114.372 3254 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.56 % Allowed : 28.45 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.30), residues: 798 helix: 1.75 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -1.32 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 573 HIS 0.003 0.001 HIS B 587 PHE 0.016 0.001 PHE B 511 TYR 0.022 0.001 TYR A 518 ARG 0.005 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.10976 ( 461) hydrogen bonds : angle 4.48969 ( 1377) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.62336 ( 4) covalent geometry : bond 0.00308 ( 7512) covalent geometry : angle 0.67500 (10166) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 0.723 Fit side-chains REVERT: A 508 MET cc_start: 0.6575 (tpp) cc_final: 0.6269 (tpp) REVERT: B 452 GLN cc_start: 0.8102 (tt0) cc_final: 0.7884 (tt0) REVERT: B 504 HIS cc_start: 0.6191 (t-90) cc_final: 0.5898 (t-90) outliers start: 4 outliers final: 3 residues processed: 155 average time/residue: 0.1911 time to fit residues: 39.6349 Evaluate side-chains 139 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 394 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 614 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.179711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138598 restraints weight = 8682.587| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.42 r_work: 0.3560 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7514 Z= 0.176 Angle : 0.651 9.830 10170 Z= 0.319 Chirality : 0.043 0.358 1094 Planarity : 0.004 0.056 1172 Dihedral : 12.957 99.092 1761 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.65 % Allowed : 24.23 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.29), residues: 798 helix: 1.81 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.33 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 514 HIS 0.004 0.001 HIS A 476 PHE 0.021 0.002 PHE A 487 TYR 0.020 0.002 TYR A 518 ARG 0.004 0.001 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.04946 ( 461) hydrogen bonds : angle 4.19825 ( 1377) SS BOND : bond 0.00395 ( 2) SS BOND : angle 0.64729 ( 4) covalent geometry : bond 0.00404 ( 7512) covalent geometry : angle 0.65074 (10166) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.782 Fit side-chains REVERT: A 298 ASN cc_start: 0.8336 (t0) cc_final: 0.8130 (t0) REVERT: A 489 MET cc_start: 0.7617 (tpt) cc_final: 0.7351 (tpt) REVERT: A 516 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8380 (p) REVERT: A 548 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7527 (mpp80) REVERT: B 345 TYR cc_start: 0.8140 (p90) cc_final: 0.7589 (p90) REVERT: B 352 TYR cc_start: 0.8488 (m-80) cc_final: 0.8095 (m-80) REVERT: B 423 TRP cc_start: 0.6864 (m100) cc_final: 0.6435 (m100) REVERT: B 429 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.6928 (tt) REVERT: B 453 CYS cc_start: 0.7974 (m) cc_final: 0.7743 (m) REVERT: B 489 MET cc_start: 0.7781 (tpt) cc_final: 0.7392 (tpt) REVERT: B 504 HIS cc_start: 0.6284 (t-90) cc_final: 0.5353 (t-90) REVERT: B 516 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8441 (p) REVERT: B 525 THR cc_start: 0.7501 (p) cc_final: 0.7196 (p) REVERT: B 530 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9005 (mp) outliers start: 33 outliers final: 16 residues processed: 170 average time/residue: 0.1861 time to fit residues: 44.6732 Evaluate side-chains 160 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.175827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.135234 restraints weight = 8792.376| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.36 r_work: 0.3513 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7514 Z= 0.207 Angle : 0.664 9.386 10170 Z= 0.326 Chirality : 0.045 0.348 1094 Planarity : 0.004 0.055 1172 Dihedral : 12.915 99.174 1757 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 6.62 % Allowed : 24.23 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.29), residues: 798 helix: 1.79 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -1.39 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 514 HIS 0.006 0.001 HIS A 476 PHE 0.028 0.002 PHE A 487 TYR 0.024 0.002 TYR A 518 ARG 0.004 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 461) hydrogen bonds : angle 4.30248 ( 1377) SS BOND : bond 0.00351 ( 2) SS BOND : angle 0.63213 ( 4) covalent geometry : bond 0.00486 ( 7512) covalent geometry : angle 0.66447 (10166) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.831 Fit side-chains REVERT: A 282 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8130 (mt) REVERT: A 298 ASN cc_start: 0.8368 (t0) cc_final: 0.8121 (t0) REVERT: A 484 SER cc_start: 0.8326 (t) cc_final: 0.8065 (p) REVERT: A 489 MET cc_start: 0.7733 (tpt) cc_final: 0.7381 (tpt) REVERT: A 516 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8413 (p) REVERT: B 236 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7222 (mtm180) REVERT: B 345 TYR cc_start: 0.8310 (p90) cc_final: 0.7747 (p90) REVERT: B 373 TRP cc_start: 0.8369 (t60) cc_final: 0.8151 (t60) REVERT: B 453 CYS cc_start: 0.8031 (m) cc_final: 0.7723 (m) REVERT: B 489 MET cc_start: 0.8040 (tpt) cc_final: 0.7647 (tpt) REVERT: B 504 HIS cc_start: 0.6596 (t-90) cc_final: 0.6383 (t-90) REVERT: B 508 MET cc_start: 0.6258 (tpp) cc_final: 0.5619 (tpt) REVERT: B 516 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8477 (p) REVERT: B 525 THR cc_start: 0.7503 (p) cc_final: 0.7188 (p) REVERT: B 528 TRP cc_start: 0.7920 (t-100) cc_final: 0.7667 (t60) REVERT: B 530 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9032 (mp) REVERT: B 618 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7702 (p0) outliers start: 47 outliers final: 22 residues processed: 183 average time/residue: 0.1733 time to fit residues: 43.7090 Evaluate side-chains 165 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 5 optimal weight: 0.1980 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 0.0070 chunk 68 optimal weight: 1.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 452 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS B 387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.179955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139755 restraints weight = 8765.692| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.41 r_work: 0.3584 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.003 0.038 7514 Z= 0.133 Angle : 0.600 8.362 10170 Z= 0.297 Chirality : 0.042 0.356 1094 Planarity : 0.004 0.055 1172 Dihedral : 12.701 96.563 1757 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.49 % Allowed : 25.35 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.30), residues: 798 helix: 2.00 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.32 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 514 HIS 0.002 0.001 HIS A 504 PHE 0.026 0.001 PHE A 487 TYR 0.021 0.001 TYR A 518 ARG 0.004 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 461) hydrogen bonds : angle 4.11039 ( 1377) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.50269 ( 4) covalent geometry : bond 0.00290 ( 7512) covalent geometry : angle 0.59971 (10166) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 298 ASN cc_start: 0.8324 (t0) cc_final: 0.8028 (t0) REVERT: A 489 MET cc_start: 0.7753 (tpt) cc_final: 0.7538 (tpt) REVERT: A 516 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8354 (p) REVERT: A 613 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8829 (tm-30) REVERT: B 282 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7995 (mt) REVERT: B 345 TYR cc_start: 0.8270 (p90) cc_final: 0.7649 (p90) REVERT: B 373 TRP cc_start: 0.8293 (t60) cc_final: 0.8035 (t60) REVERT: B 453 CYS cc_start: 0.7895 (m) cc_final: 0.7575 (m) REVERT: B 489 MET cc_start: 0.8018 (tpt) cc_final: 0.7713 (tpt) REVERT: B 504 HIS cc_start: 0.6587 (t-90) cc_final: 0.6353 (t-90) REVERT: B 516 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8437 (p) REVERT: B 530 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9018 (mp) outliers start: 39 outliers final: 22 residues processed: 186 average time/residue: 0.1624 time to fit residues: 42.1436 Evaluate side-chains 173 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.174569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.135024 restraints weight = 8726.609| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.33 r_work: 0.3510 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7514 Z= 0.206 Angle : 0.662 9.310 10170 Z= 0.326 Chirality : 0.045 0.335 1094 Planarity : 0.004 0.055 1172 Dihedral : 13.032 96.098 1757 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.62 % Allowed : 24.93 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.30), residues: 798 helix: 1.80 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.19 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 373 HIS 0.005 0.001 HIS A 476 PHE 0.024 0.002 PHE A 487 TYR 0.024 0.002 TYR A 518 ARG 0.004 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04992 ( 461) hydrogen bonds : angle 4.28443 ( 1377) SS BOND : bond 0.00348 ( 2) SS BOND : angle 0.54781 ( 4) covalent geometry : bond 0.00487 ( 7512) covalent geometry : angle 0.66228 (10166) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 282 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8124 (mt) REVERT: A 298 ASN cc_start: 0.8362 (t0) cc_final: 0.8111 (t0) REVERT: A 345 TYR cc_start: 0.8141 (p90) cc_final: 0.7649 (p90) REVERT: A 516 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8395 (p) REVERT: A 518 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6891 (t80) REVERT: A 528 TRP cc_start: 0.8148 (t-100) cc_final: 0.7864 (t60) REVERT: A 613 GLU cc_start: 0.9312 (tm-30) cc_final: 0.8793 (tm-30) REVERT: B 236 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7233 (mtm180) REVERT: B 282 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8145 (mt) REVERT: B 345 TYR cc_start: 0.8310 (p90) cc_final: 0.7734 (p90) REVERT: B 453 CYS cc_start: 0.7999 (m) cc_final: 0.7637 (m) REVERT: B 489 MET cc_start: 0.8139 (tpt) cc_final: 0.7937 (tpt) REVERT: B 516 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8416 (p) REVERT: B 525 THR cc_start: 0.7555 (p) cc_final: 0.7200 (p) REVERT: B 528 TRP cc_start: 0.7933 (t-100) cc_final: 0.7561 (t60) REVERT: B 530 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9011 (mp) REVERT: B 618 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7839 (p0) outliers start: 47 outliers final: 30 residues processed: 181 average time/residue: 0.1831 time to fit residues: 46.1723 Evaluate side-chains 180 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.176222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136043 restraints weight = 8709.005| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.37 r_work: 0.3524 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7514 Z= 0.180 Angle : 0.645 8.223 10170 Z= 0.322 Chirality : 0.045 0.329 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.931 95.471 1757 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.62 % Allowed : 26.06 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.30), residues: 798 helix: 1.82 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.19 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 373 HIS 0.003 0.001 HIS B 499 PHE 0.029 0.002 PHE A 487 TYR 0.019 0.002 TYR A 518 ARG 0.004 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 461) hydrogen bonds : angle 4.22957 ( 1377) SS BOND : bond 0.00291 ( 2) SS BOND : angle 0.49955 ( 4) covalent geometry : bond 0.00424 ( 7512) covalent geometry : angle 0.64515 (10166) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 282 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8125 (mt) REVERT: A 298 ASN cc_start: 0.8310 (t0) cc_final: 0.8043 (t0) REVERT: A 345 TYR cc_start: 0.8169 (p90) cc_final: 0.7603 (p90) REVERT: A 489 MET cc_start: 0.7850 (tpt) cc_final: 0.7462 (tpt) REVERT: A 516 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8390 (p) REVERT: A 528 TRP cc_start: 0.8171 (t-100) cc_final: 0.7890 (t-100) REVERT: B 236 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7185 (mtm180) REVERT: B 282 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8112 (mt) REVERT: B 345 TYR cc_start: 0.8347 (p90) cc_final: 0.7735 (p90) REVERT: B 423 TRP cc_start: 0.6912 (m100) cc_final: 0.6269 (m100) REVERT: B 453 CYS cc_start: 0.7975 (m) cc_final: 0.7613 (m) REVERT: B 504 HIS cc_start: 0.6565 (t-90) cc_final: 0.6306 (t-90) REVERT: B 508 MET cc_start: 0.6428 (tpp) cc_final: 0.5663 (tpt) REVERT: B 516 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 525 THR cc_start: 0.7544 (p) cc_final: 0.7205 (p) REVERT: B 528 TRP cc_start: 0.7980 (t-100) cc_final: 0.7596 (t60) REVERT: B 530 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8998 (mp) outliers start: 47 outliers final: 33 residues processed: 172 average time/residue: 0.2150 time to fit residues: 51.1304 Evaluate side-chains 180 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.176067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136833 restraints weight = 8792.735| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.33 r_work: 0.3532 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7514 Z= 0.171 Angle : 0.644 7.888 10170 Z= 0.322 Chirality : 0.044 0.320 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.757 94.406 1757 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 6.90 % Allowed : 25.92 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.30), residues: 798 helix: 1.87 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.14 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 373 HIS 0.003 0.001 HIS B 499 PHE 0.029 0.002 PHE A 487 TYR 0.019 0.001 TYR A 518 ARG 0.005 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 461) hydrogen bonds : angle 4.20407 ( 1377) SS BOND : bond 0.00423 ( 2) SS BOND : angle 0.69891 ( 4) covalent geometry : bond 0.00397 ( 7512) covalent geometry : angle 0.64357 (10166) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 0.780 Fit side-chains REVERT: A 282 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8098 (mt) REVERT: A 298 ASN cc_start: 0.8308 (t0) cc_final: 0.8023 (t0) REVERT: A 345 TYR cc_start: 0.8139 (p90) cc_final: 0.7249 (p90) REVERT: A 489 MET cc_start: 0.7828 (tpt) cc_final: 0.7612 (tpt) REVERT: A 516 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8398 (p) REVERT: A 518 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6807 (t80) REVERT: A 528 TRP cc_start: 0.8193 (t-100) cc_final: 0.7903 (t-100) REVERT: B 236 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7179 (mtm180) REVERT: B 282 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8093 (mt) REVERT: B 345 TYR cc_start: 0.8299 (p90) cc_final: 0.7800 (p90) REVERT: B 423 TRP cc_start: 0.6929 (m100) cc_final: 0.6350 (m100) REVERT: B 453 CYS cc_start: 0.7940 (m) cc_final: 0.7554 (m) REVERT: B 489 MET cc_start: 0.8106 (tpt) cc_final: 0.7499 (tpt) REVERT: B 504 HIS cc_start: 0.6619 (t-90) cc_final: 0.6343 (t-90) REVERT: B 508 MET cc_start: 0.6503 (tpp) cc_final: 0.5767 (tpt) REVERT: B 528 TRP cc_start: 0.7980 (t-100) cc_final: 0.7698 (t60) REVERT: B 530 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8981 (mp) REVERT: B 618 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7783 (p0) outliers start: 49 outliers final: 33 residues processed: 177 average time/residue: 0.1796 time to fit residues: 44.0130 Evaluate side-chains 180 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 0.0370 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 314 GLN B 387 HIS ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.177408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137764 restraints weight = 8802.995| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.36 r_work: 0.3544 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7514 Z= 0.157 Angle : 0.635 8.612 10170 Z= 0.320 Chirality : 0.044 0.315 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.674 93.719 1757 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.92 % Allowed : 27.18 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.30), residues: 798 helix: 1.89 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.10 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 373 HIS 0.006 0.001 HIS A 387 PHE 0.036 0.002 PHE A 487 TYR 0.020 0.002 TYR B 467 ARG 0.005 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04746 ( 461) hydrogen bonds : angle 4.19184 ( 1377) SS BOND : bond 0.00370 ( 2) SS BOND : angle 0.65993 ( 4) covalent geometry : bond 0.00359 ( 7512) covalent geometry : angle 0.63503 (10166) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.718 Fit side-chains REVERT: A 282 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8087 (mt) REVERT: A 298 ASN cc_start: 0.8277 (t0) cc_final: 0.7993 (t0) REVERT: A 345 TYR cc_start: 0.8191 (p90) cc_final: 0.7684 (p90) REVERT: A 489 MET cc_start: 0.7793 (tpt) cc_final: 0.7500 (tpt) REVERT: A 516 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8385 (p) REVERT: A 528 TRP cc_start: 0.8219 (t-100) cc_final: 0.7906 (t-100) REVERT: B 282 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8090 (mt) REVERT: B 345 TYR cc_start: 0.8304 (p90) cc_final: 0.7868 (p90) REVERT: B 423 TRP cc_start: 0.6877 (m100) cc_final: 0.6291 (m100) REVERT: B 453 CYS cc_start: 0.7834 (m) cc_final: 0.7448 (m) REVERT: B 459 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7556 (mmm160) REVERT: B 489 MET cc_start: 0.8069 (tpt) cc_final: 0.7560 (tpt) REVERT: B 504 HIS cc_start: 0.6623 (t-90) cc_final: 0.6342 (t-90) REVERT: B 508 MET cc_start: 0.6458 (tpp) cc_final: 0.5707 (tpt) REVERT: B 528 TRP cc_start: 0.8065 (t-100) cc_final: 0.7706 (t60) REVERT: B 530 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8947 (mp) REVERT: B 618 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7792 (p0) outliers start: 42 outliers final: 30 residues processed: 169 average time/residue: 0.1612 time to fit residues: 38.1383 Evaluate side-chains 175 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.176398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.136638 restraints weight = 8808.974| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.36 r_work: 0.3531 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7514 Z= 0.179 Angle : 0.652 7.974 10170 Z= 0.327 Chirality : 0.045 0.301 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.684 93.220 1757 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.92 % Allowed : 27.32 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.30), residues: 798 helix: 1.83 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.14 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 514 HIS 0.003 0.001 HIS B 499 PHE 0.038 0.002 PHE A 487 TYR 0.022 0.002 TYR B 467 ARG 0.006 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 461) hydrogen bonds : angle 4.25178 ( 1377) SS BOND : bond 0.00368 ( 2) SS BOND : angle 0.67502 ( 4) covalent geometry : bond 0.00420 ( 7512) covalent geometry : angle 0.65205 (10166) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.816 Fit side-chains REVERT: A 282 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8108 (mt) REVERT: A 298 ASN cc_start: 0.8289 (t0) cc_final: 0.8000 (t0) REVERT: A 345 TYR cc_start: 0.8263 (p90) cc_final: 0.7676 (p90) REVERT: A 516 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8397 (p) REVERT: A 518 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6864 (t80) REVERT: A 528 TRP cc_start: 0.8224 (t-100) cc_final: 0.7907 (t-100) REVERT: B 263 ARG cc_start: 0.7072 (mtp85) cc_final: 0.6743 (mtp85) REVERT: B 282 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8106 (mt) REVERT: B 345 TYR cc_start: 0.8320 (p90) cc_final: 0.7951 (p90) REVERT: B 423 TRP cc_start: 0.6947 (m100) cc_final: 0.6381 (m100) REVERT: B 453 CYS cc_start: 0.7812 (m) cc_final: 0.7450 (m) REVERT: B 459 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7570 (mmm160) REVERT: B 489 MET cc_start: 0.8161 (tpt) cc_final: 0.7698 (tpt) REVERT: B 504 HIS cc_start: 0.6654 (t-90) cc_final: 0.6374 (t-90) REVERT: B 528 TRP cc_start: 0.8094 (t-100) cc_final: 0.7681 (t60) REVERT: B 530 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8931 (mp) REVERT: B 618 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7823 (p0) outliers start: 42 outliers final: 34 residues processed: 168 average time/residue: 0.1627 time to fit residues: 38.1996 Evaluate side-chains 181 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 63 optimal weight: 0.0980 chunk 5 optimal weight: 0.0980 chunk 22 optimal weight: 0.1980 chunk 44 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 79 optimal weight: 0.0670 overall best weight: 0.1096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 294 GLN B 387 HIS B 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.180979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142389 restraints weight = 8774.250| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.36 r_work: 0.3605 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7514 Z= 0.131 Angle : 0.633 10.079 10170 Z= 0.318 Chirality : 0.043 0.297 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.383 91.855 1757 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.79 % Allowed : 28.73 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.30), residues: 798 helix: 2.03 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.08 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 514 HIS 0.009 0.001 HIS A 387 PHE 0.037 0.001 PHE A 487 TYR 0.021 0.001 TYR B 467 ARG 0.006 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 461) hydrogen bonds : angle 4.13690 ( 1377) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.48298 ( 4) covalent geometry : bond 0.00279 ( 7512) covalent geometry : angle 0.63268 (10166) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.814 Fit side-chains REVERT: A 345 TYR cc_start: 0.8264 (p90) cc_final: 0.7817 (p90) REVERT: A 423 TRP cc_start: 0.7287 (m100) cc_final: 0.6952 (m100) REVERT: A 472 ARG cc_start: 0.7204 (ttt180) cc_final: 0.6836 (ttt90) REVERT: A 489 MET cc_start: 0.7796 (tpt) cc_final: 0.7299 (tpt) REVERT: A 516 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8387 (p) REVERT: A 528 TRP cc_start: 0.8122 (t-100) cc_final: 0.7855 (t60) REVERT: B 263 ARG cc_start: 0.7063 (mtp85) cc_final: 0.6716 (mtp85) REVERT: B 345 TYR cc_start: 0.8281 (p90) cc_final: 0.7810 (p90) REVERT: B 423 TRP cc_start: 0.6814 (m100) cc_final: 0.6084 (m100) REVERT: B 453 CYS cc_start: 0.7681 (m) cc_final: 0.7388 (m) REVERT: B 459 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7466 (mmm160) REVERT: B 489 MET cc_start: 0.8039 (tpt) cc_final: 0.7598 (tpt) REVERT: B 504 HIS cc_start: 0.6685 (t-90) cc_final: 0.6424 (t-90) REVERT: B 530 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8858 (mp) REVERT: B 618 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7652 (p0) outliers start: 34 outliers final: 22 residues processed: 169 average time/residue: 0.1794 time to fit residues: 41.5497 Evaluate side-chains 168 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 76 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.0970 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 42 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.180159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140630 restraints weight = 8647.593| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.36 r_work: 0.3584 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7514 Z= 0.150 Angle : 0.636 9.540 10170 Z= 0.320 Chirality : 0.044 0.282 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.341 91.351 1757 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.51 % Allowed : 29.58 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.30), residues: 798 helix: 2.00 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.13 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 514 HIS 0.003 0.001 HIS B 499 PHE 0.038 0.001 PHE A 487 TYR 0.022 0.001 TYR B 467 ARG 0.005 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 461) hydrogen bonds : angle 4.13626 ( 1377) SS BOND : bond 0.00220 ( 2) SS BOND : angle 0.52078 ( 4) covalent geometry : bond 0.00342 ( 7512) covalent geometry : angle 0.63642 (10166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4103.09 seconds wall clock time: 72 minutes 38.23 seconds (4358.23 seconds total)