Starting phenix.real_space_refine on Mon Apr 28 09:15:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9inf_60705/04_2025/9inf_60705.cif Found real_map, /net/cci-nas-00/data/ceres_data/9inf_60705/04_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_60705/04_2025/9inf_60705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9inf_60705/04_2025/9inf_60705.map" model { file = "/net/cci-nas-00/data/ceres_data/9inf_60705/04_2025/9inf_60705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9inf_60705/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 9.19, per 1000 atoms: 1.26 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: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.86 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: 3.53 Time building geometry restraints manager: 2.86 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: 0.000 Normalize map: mean=0, sd=1: 219.140 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 27.400 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:4.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 252.300 ------------------------------------------------------------------------------- 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 : 2.703 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: 0.3190 time to fit residues: 68.4551 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 : 1.064 ------------------------------------------------------------------------------- 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 = 0.179712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138602 restraints weight = 8682.585| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.42 r_work: 0.3563 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 0.041 7514 Z= 0.176 Angle : 0.650 9.832 10170 Z= 0.319 Chirality : 0.043 0.358 1094 Planarity : 0.004 0.056 1172 Dihedral : 12.956 99.093 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 0.04944 ( 461) hydrogen bonds : angle 4.19829 ( 1377) SS BOND : bond 0.00392 ( 2) SS BOND : angle 0.64369 ( 4) covalent geometry : bond 0.00404 ( 7512) covalent geometry : angle 0.65042 (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 : 0.792 Fit side-chains REVERT: A 298 ASN cc_start: 0.8342 (t0) cc_final: 0.8134 (t0) REVERT: A 489 MET cc_start: 0.7613 (tpt) cc_final: 0.7351 (tpt) REVERT: A 516 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8382 (p) REVERT: A 548 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7538 (mpp80) REVERT: B 345 TYR cc_start: 0.8131 (p90) cc_final: 0.7580 (p90) REVERT: B 352 TYR cc_start: 0.8496 (m-80) cc_final: 0.8102 (m-80) REVERT: B 423 TRP cc_start: 0.6869 (m100) cc_final: 0.6439 (m100) REVERT: B 429 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6920 (tt) REVERT: B 453 CYS cc_start: 0.7976 (m) cc_final: 0.7744 (m) REVERT: B 489 MET cc_start: 0.7778 (tpt) cc_final: 0.7393 (tpt) REVERT: B 504 HIS cc_start: 0.6305 (t-90) cc_final: 0.5377 (t-90) REVERT: B 516 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8446 (p) REVERT: B 525 THR cc_start: 0.7512 (p) cc_final: 0.7208 (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: 0.1624 time to fit residues: 38.6278 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 : 0.807 ------------------------------------------------------------------------------- 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: 0.4980 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.176384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.136401 restraints weight = 8789.882| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.34 r_work: 0.3528 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1465 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= 0.192 Angle : 0.650 9.117 10170 Z= 0.319 Chirality : 0.044 0.350 1094 Planarity : 0.004 0.055 1172 Dihedral : 12.834 99.095 1757 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 6.62 % Allowed : 24.08 % Favored : 69.30 % 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: 1.79 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.29 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 514 HIS 0.007 0.001 HIS B 499 PHE 0.028 0.002 PHE A 487 TYR 0.023 0.002 TYR A 518 ARG 0.003 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.04948 ( 461) hydrogen bonds : angle 4.26556 ( 1377) SS BOND : bond 0.00350 ( 2) SS BOND : angle 0.59509 ( 4) covalent geometry : bond 0.00450 ( 7512) covalent geometry : angle 0.64984 (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 202 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 0.892 Fit side-chains REVERT: A 282 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8137 (mt) REVERT: A 298 ASN cc_start: 0.8361 (t0) cc_final: 0.8111 (t0) REVERT: A 489 MET cc_start: 0.7721 (tpt) cc_final: 0.7365 (tpt) REVERT: A 516 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8404 (p) REVERT: A 613 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8994 (tm-30) REVERT: B 236 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7195 (mtm180) REVERT: B 345 TYR cc_start: 0.8303 (p90) cc_final: 0.7752 (p90) REVERT: B 373 TRP cc_start: 0.8337 (t60) cc_final: 0.8124 (t60) REVERT: B 423 TRP cc_start: 0.6897 (m100) cc_final: 0.6554 (m100) REVERT: B 453 CYS cc_start: 0.7967 (m) cc_final: 0.7652 (m) REVERT: B 489 MET cc_start: 0.8030 (tpt) cc_final: 0.7619 (tpt) REVERT: B 504 HIS cc_start: 0.6628 (t-90) cc_final: 0.6416 (t-90) REVERT: B 508 MET cc_start: 0.6275 (tpp) cc_final: 0.5612 (tpt) REVERT: B 516 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8473 (p) REVERT: B 525 THR cc_start: 0.7501 (p) cc_final: 0.7180 (p) REVERT: B 528 TRP cc_start: 0.7894 (t-100) cc_final: 0.7558 (t60) REVERT: B 530 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9018 (mp) REVERT: B 618 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7685 (p0) outliers start: 47 outliers final: 21 residues processed: 185 average time/residue: 0.1956 time to fit residues: 49.8307 Evaluate side-chains 170 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 57 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 5 optimal weight: 0.0870 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.178957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.138324 restraints weight = 8767.540| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.38 r_work: 0.3550 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7514 Z= 0.156 Angle : 0.622 8.964 10170 Z= 0.308 Chirality : 0.044 0.351 1094 Planarity : 0.004 0.055 1172 Dihedral : 12.771 97.185 1757 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.35 % Allowed : 25.49 % 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: 1.61 (0.30), residues: 798 helix: 1.94 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -1.33 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 514 HIS 0.003 0.001 HIS A 476 PHE 0.030 0.001 PHE A 487 TYR 0.023 0.001 TYR A 518 ARG 0.004 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.04733 ( 461) hydrogen bonds : angle 4.17170 ( 1377) SS BOND : bond 0.00362 ( 2) SS BOND : angle 0.70306 ( 4) covalent geometry : bond 0.00357 ( 7512) covalent geometry : angle 0.62206 (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 195 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 298 ASN cc_start: 0.8347 (t0) cc_final: 0.8081 (t0) REVERT: A 516 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8394 (p) REVERT: A 613 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8747 (tm-30) REVERT: B 282 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8084 (mt) REVERT: B 345 TYR cc_start: 0.8282 (p90) cc_final: 0.7726 (p90) REVERT: B 373 TRP cc_start: 0.8315 (t60) cc_final: 0.8108 (t60) REVERT: B 453 CYS cc_start: 0.7928 (m) cc_final: 0.7618 (m) REVERT: B 489 MET cc_start: 0.8062 (tpt) cc_final: 0.7747 (tpt) REVERT: B 516 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8452 (p) REVERT: B 525 THR cc_start: 0.7423 (p) cc_final: 0.7118 (p) REVERT: B 528 TRP cc_start: 0.7903 (t-100) cc_final: 0.7672 (t60) REVERT: B 530 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9027 (mp) outliers start: 38 outliers final: 23 residues processed: 178 average time/residue: 0.1628 time to fit residues: 40.9336 Evaluate side-chains 170 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 0.7980 chunk 25 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.175973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135636 restraints weight = 8714.714| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.38 r_work: 0.3517 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7514 Z= 0.195 Angle : 0.657 8.957 10170 Z= 0.325 Chirality : 0.045 0.339 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.974 96.383 1757 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.76 % Allowed : 24.93 % Favored : 68.31 % 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: 1.56 (0.30), residues: 798 helix: 1.83 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -1.20 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 514 HIS 0.004 0.001 HIS A 476 PHE 0.031 0.002 PHE A 487 TYR 0.023 0.002 TYR A 518 ARG 0.004 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 461) hydrogen bonds : angle 4.26629 ( 1377) SS BOND : bond 0.00449 ( 2) SS BOND : angle 0.78055 ( 4) covalent geometry : bond 0.00456 ( 7512) covalent geometry : angle 0.65658 (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 195 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 282 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8113 (mt) REVERT: A 298 ASN cc_start: 0.8369 (t0) cc_final: 0.8110 (t0) REVERT: A 489 MET cc_start: 0.7842 (tpt) cc_final: 0.7438 (tpt) REVERT: A 516 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 528 TRP cc_start: 0.8140 (t-100) cc_final: 0.7864 (t60) REVERT: B 236 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7200 (mtm180) REVERT: B 282 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8133 (mt) REVERT: B 345 TYR cc_start: 0.8344 (p90) cc_final: 0.7786 (p90) REVERT: B 373 TRP cc_start: 0.8349 (t60) cc_final: 0.8143 (t60) REVERT: B 453 CYS cc_start: 0.7976 (m) cc_final: 0.7610 (m) REVERT: B 489 MET cc_start: 0.8124 (tpt) cc_final: 0.7897 (tpt) REVERT: B 504 HIS cc_start: 0.6576 (t-90) cc_final: 0.6324 (t-90) REVERT: B 516 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8453 (p) REVERT: B 525 THR cc_start: 0.7459 (p) cc_final: 0.7151 (p) REVERT: B 528 TRP cc_start: 0.8055 (t-100) cc_final: 0.7639 (t60) REVERT: B 530 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9006 (mp) REVERT: B 618 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7820 (p0) outliers start: 48 outliers final: 29 residues processed: 177 average time/residue: 0.2316 time to fit residues: 56.7752 Evaluate side-chains 174 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 454 ILE 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 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 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: 0.4980 chunk 21 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 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: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.176915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136156 restraints weight = 8684.588| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.38 r_work: 0.3525 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7514 Z= 0.181 Angle : 0.641 8.590 10170 Z= 0.320 Chirality : 0.044 0.331 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.919 95.570 1757 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 7.18 % Allowed : 25.07 % Favored : 67.75 % 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: 1.63 (0.30), residues: 798 helix: 1.89 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -1.19 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 373 HIS 0.003 0.001 HIS A 476 PHE 0.030 0.002 PHE A 487 TYR 0.020 0.002 TYR A 518 ARG 0.005 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 461) hydrogen bonds : angle 4.22316 ( 1377) SS BOND : bond 0.00388 ( 2) SS BOND : angle 0.74831 ( 4) covalent geometry : bond 0.00423 ( 7512) covalent geometry : angle 0.64064 (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 196 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 1.648 Fit side-chains revert: symmetry clash REVERT: A 282 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8126 (mt) REVERT: A 298 ASN cc_start: 0.8312 (t0) cc_final: 0.8047 (t0) REVERT: A 345 TYR cc_start: 0.8163 (p90) cc_final: 0.7584 (p90) REVERT: A 489 MET cc_start: 0.7922 (tpt) cc_final: 0.7627 (tpt) REVERT: A 516 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8410 (p) REVERT: A 518 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6781 (t80) REVERT: A 528 TRP cc_start: 0.8175 (t-100) cc_final: 0.7901 (t60) REVERT: B 236 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7177 (mtm180) REVERT: B 282 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8115 (mt) REVERT: B 345 TYR cc_start: 0.8352 (p90) cc_final: 0.7867 (p90) REVERT: B 373 TRP cc_start: 0.8353 (t60) cc_final: 0.8105 (t60) REVERT: B 453 CYS cc_start: 0.7941 (m) cc_final: 0.7558 (m) REVERT: B 504 HIS cc_start: 0.6586 (t-90) cc_final: 0.6293 (t-90) REVERT: B 508 MET cc_start: 0.6357 (tpp) cc_final: 0.5612 (tpt) REVERT: B 516 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8458 (p) REVERT: B 525 THR cc_start: 0.7437 (p) cc_final: 0.7129 (p) REVERT: B 528 TRP cc_start: 0.8073 (t-100) cc_final: 0.7621 (t60) REVERT: B 530 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9000 (mp) REVERT: B 618 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7796 (p0) outliers start: 51 outliers final: 32 residues processed: 178 average time/residue: 0.2202 time to fit residues: 54.4474 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 : 0.818 ------------------------------------------------------------------------------- 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 454 ILE 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 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 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 Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 0.0770 chunk 18 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 63 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.138339 restraints weight = 8723.393| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.37 r_work: 0.3560 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7514 Z= 0.147 Angle : 0.623 7.846 10170 Z= 0.313 Chirality : 0.043 0.325 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.612 94.044 1757 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 6.34 % Allowed : 26.34 % 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: 1.81 (0.30), residues: 798 helix: 2.02 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.15 (0.44), residues: 214 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 0.031 0.001 PHE A 487 TYR 0.017 0.001 TYR B 467 ARG 0.005 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 461) hydrogen bonds : angle 4.13838 ( 1377) SS BOND : bond 0.00295 ( 2) SS BOND : angle 0.64951 ( 4) covalent geometry : bond 0.00330 ( 7512) covalent geometry : angle 0.62326 (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 199 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 298 ASN cc_start: 0.8284 (t0) cc_final: 0.7990 (t0) REVERT: A 345 TYR cc_start: 0.8144 (p90) cc_final: 0.7599 (p90) REVERT: A 516 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8410 (p) REVERT: A 518 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.6834 (t80) REVERT: B 236 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7068 (mtm180) REVERT: B 282 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8030 (mt) REVERT: B 345 TYR cc_start: 0.8307 (p90) cc_final: 0.7833 (p90) REVERT: B 423 TRP cc_start: 0.6968 (m100) cc_final: 0.6455 (m100) REVERT: B 453 CYS cc_start: 0.7829 (m) cc_final: 0.7431 (m) REVERT: B 459 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7561 (mmm160) REVERT: B 489 MET cc_start: 0.8124 (tpt) cc_final: 0.7386 (tpt) REVERT: B 508 MET cc_start: 0.6452 (tpp) cc_final: 0.5744 (tpt) REVERT: B 516 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8542 (p) REVERT: B 528 TRP cc_start: 0.7968 (t-100) cc_final: 0.7614 (t60) REVERT: B 530 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8978 (mp) REVERT: B 618 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7681 (p0) outliers start: 45 outliers final: 28 residues processed: 186 average time/residue: 0.1994 time to fit residues: 51.4777 Evaluate side-chains 177 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 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 454 ILE 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 0.0000 chunk 36 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 0.2980 chunk 1 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.0770 overall best weight: 0.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.181173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141423 restraints weight = 8748.475| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.41 r_work: 0.3599 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1975 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= 0.132 Angle : 0.619 8.548 10170 Z= 0.312 Chirality : 0.043 0.320 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.389 92.897 1757 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.65 % Allowed : 28.87 % 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: 1.89 (0.30), residues: 798 helix: 2.07 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.08 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 373 HIS 0.003 0.001 HIS B 499 PHE 0.034 0.001 PHE A 487 TYR 0.019 0.001 TYR B 467 ARG 0.006 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 461) hydrogen bonds : angle 4.10984 ( 1377) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.52408 ( 4) covalent geometry : bond 0.00285 ( 7512) covalent geometry : angle 0.61881 (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 182 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.946 Fit side-chains REVERT: A 298 ASN cc_start: 0.8263 (t0) cc_final: 0.8053 (t0) REVERT: A 345 TYR cc_start: 0.8085 (p90) cc_final: 0.7631 (p90) REVERT: A 489 MET cc_start: 0.7785 (tpt) cc_final: 0.7307 (tpt) REVERT: A 516 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8383 (p) REVERT: A 571 PHE cc_start: 0.7035 (m-10) cc_final: 0.6370 (m-10) REVERT: B 263 ARG cc_start: 0.7039 (mtp85) cc_final: 0.6673 (mtp85) REVERT: B 282 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7997 (mt) REVERT: B 345 TYR cc_start: 0.8308 (p90) cc_final: 0.7923 (p90) REVERT: B 423 TRP cc_start: 0.6871 (m100) cc_final: 0.6384 (m100) REVERT: B 452 GLN cc_start: 0.8238 (tt0) cc_final: 0.7984 (tt0) REVERT: B 453 CYS cc_start: 0.7725 (m) cc_final: 0.7402 (m) REVERT: B 459 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7573 (mmm160) REVERT: B 489 MET cc_start: 0.8046 (tpt) cc_final: 0.7418 (tpt) REVERT: B 504 HIS cc_start: 0.6507 (t-90) cc_final: 0.6288 (t-90) REVERT: B 508 MET cc_start: 0.6599 (tpp) cc_final: 0.5920 (tpt) REVERT: B 530 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8893 (mp) outliers start: 33 outliers final: 23 residues processed: 172 average time/residue: 0.2245 time to fit residues: 54.3878 Evaluate side-chains 173 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 609 PHE Chi-restraints excluded: chain A residue 618 ASN 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 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 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 530 LEU Chi-restraints excluded: chain B residue 605 PHE 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: 0.7980 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137529 restraints weight = 8776.274| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.39 r_work: 0.3550 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7514 Z= 0.186 Angle : 0.651 8.179 10170 Z= 0.329 Chirality : 0.045 0.295 1094 Planarity : 0.004 0.055 1172 Dihedral : 12.506 92.641 1757 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.21 % Allowed : 28.31 % 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: 1.78 (0.30), residues: 798 helix: 1.95 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.00 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 373 HIS 0.006 0.001 HIS B 387 PHE 0.035 0.002 PHE A 487 TYR 0.022 0.002 TYR B 467 ARG 0.004 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 461) hydrogen bonds : angle 4.18975 ( 1377) SS BOND : bond 0.00310 ( 2) SS BOND : angle 0.66895 ( 4) covalent geometry : bond 0.00437 ( 7512) covalent geometry : angle 0.65113 (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 185 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 1.837 Fit side-chains REVERT: A 298 ASN cc_start: 0.8315 (t0) cc_final: 0.8024 (t0) REVERT: A 345 TYR cc_start: 0.8204 (p90) cc_final: 0.7652 (p90) REVERT: A 489 MET cc_start: 0.7755 (tpt) cc_final: 0.7291 (tpt) REVERT: A 516 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8399 (p) REVERT: B 236 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7113 (mtm180) REVERT: B 263 ARG cc_start: 0.7071 (mtp85) cc_final: 0.6668 (mtp85) REVERT: B 282 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8091 (mt) REVERT: B 345 TYR cc_start: 0.8271 (p90) cc_final: 0.7856 (p90) REVERT: B 423 TRP cc_start: 0.6923 (m100) cc_final: 0.6456 (m100) REVERT: B 453 CYS cc_start: 0.7832 (m) cc_final: 0.7458 (m) REVERT: B 459 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7592 (mmm160) REVERT: B 489 MET cc_start: 0.8085 (tpt) cc_final: 0.7639 (tpt) REVERT: B 504 HIS cc_start: 0.6542 (t-90) cc_final: 0.6308 (t-90) REVERT: B 528 TRP cc_start: 0.8019 (t-100) cc_final: 0.7613 (t-100) REVERT: B 530 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8930 (mp) REVERT: B 618 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7747 (p0) outliers start: 37 outliers final: 29 residues processed: 173 average time/residue: 0.2823 time to fit residues: 68.6871 Evaluate side-chains 175 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 253 LEU 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 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 573 TRP Chi-restraints excluded: chain A residue 609 PHE 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 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 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 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 63 optimal weight: 0.1980 chunk 5 optimal weight: 0.1980 chunk 22 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 294 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.180634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.140833 restraints weight = 8862.493| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.40 r_work: 0.3587 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2103 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= 0.143 Angle : 0.636 8.630 10170 Z= 0.319 Chirality : 0.044 0.289 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.389 91.983 1757 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.65 % Allowed : 29.15 % Favored : 66.20 % 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: 2.01 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.00 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 514 HIS 0.008 0.001 HIS B 387 PHE 0.036 0.001 PHE A 487 TYR 0.026 0.001 TYR B 467 ARG 0.005 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 461) hydrogen bonds : angle 4.12500 ( 1377) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.50628 ( 4) covalent geometry : bond 0.00318 ( 7512) covalent geometry : angle 0.63582 (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 175 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 1.102 Fit side-chains REVERT: A 298 ASN cc_start: 0.8281 (t0) cc_final: 0.8066 (t0) REVERT: A 345 TYR cc_start: 0.8185 (p90) cc_final: 0.7201 (p90) REVERT: A 489 MET cc_start: 0.7699 (tpt) cc_final: 0.7232 (tpt) REVERT: A 516 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8390 (p) REVERT: A 571 PHE cc_start: 0.7026 (m-10) cc_final: 0.6371 (m-10) REVERT: B 263 ARG cc_start: 0.7086 (mtp85) cc_final: 0.6700 (mtp85) REVERT: B 282 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8053 (mt) REVERT: B 345 TYR cc_start: 0.8282 (p90) cc_final: 0.7990 (p90) REVERT: B 423 TRP cc_start: 0.6891 (m100) cc_final: 0.6527 (m100) REVERT: B 453 CYS cc_start: 0.7766 (m) cc_final: 0.7428 (m) REVERT: B 459 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7591 (mmm160) REVERT: B 489 MET cc_start: 0.8061 (tpt) cc_final: 0.7629 (tpt) REVERT: B 504 HIS cc_start: 0.6535 (t-90) cc_final: 0.6314 (t-90) REVERT: B 528 TRP cc_start: 0.7970 (t-100) cc_final: 0.7645 (t-100) REVERT: B 530 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8884 (mp) outliers start: 33 outliers final: 29 residues processed: 164 average time/residue: 0.1686 time to fit residues: 38.5135 Evaluate side-chains 175 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU 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 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 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 530 LEU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 76 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 0.0370 chunk 42 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.179138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140067 restraints weight = 8667.895| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.34 r_work: 0.3577 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7514 Z= 0.158 Angle : 0.640 8.234 10170 Z= 0.322 Chirality : 0.044 0.271 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.394 91.453 1757 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.79 % Allowed : 29.44 % Favored : 65.77 % 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: 1.80 (0.30), residues: 798 helix: 1.98 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.04 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 514 HIS 0.003 0.001 HIS B 387 PHE 0.036 0.001 PHE A 487 TYR 0.029 0.002 TYR B 467 ARG 0.004 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 461) hydrogen bonds : angle 4.15924 ( 1377) SS BOND : bond 0.00206 ( 2) SS BOND : angle 0.50785 ( 4) covalent geometry : bond 0.00367 ( 7512) covalent geometry : angle 0.64032 (10166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5356.54 seconds wall clock time: 99 minutes 23.73 seconds (5963.73 seconds total)