Starting phenix.real_space_refine on Fri Aug 22 17:54:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cn0_30412/08_2025/7cn0_30412.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cn0_30412/08_2025/7cn0_30412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cn0_30412/08_2025/7cn0_30412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cn0_30412/08_2025/7cn0_30412.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cn0_30412/08_2025/7cn0_30412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cn0_30412/08_2025/7cn0_30412.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 1.000 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 K 2 8.98 5 S 24 5.16 5 C 4412 2.51 5 N 1076 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6602 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1650 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 5 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 1.19, per 1000 atoms: 0.18 Number of scatterers: 6602 At special positions: 0 Unit cell: (106.964, 106.964, 77.792, 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) K 2 19.00 S 24 16.00 O 1088 8.00 N 1076 7.00 C 4412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 348.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 77.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 404 through 431 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.874A pdb=" N MET A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 497 removed outlier: 4.407A pdb=" N VAL A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.796A pdb=" N ARG A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 533 through 538' Processing helix chain 'A' and resid 548 through 575 Processing helix chain 'A' and resid 585 through 593 removed outlier: 3.795A pdb=" N ASP A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 624 removed outlier: 4.002A pdb=" N ALA A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 666 removed outlier: 4.058A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 431 Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 456 through 473 removed outlier: 3.874A pdb=" N MET B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 removed outlier: 4.407A pdb=" N VAL B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'B' and resid 522 through 532 Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.796A pdb=" N ARG B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 538' Processing helix chain 'B' and resid 548 through 575 Processing helix chain 'B' and resid 585 through 593 removed outlier: 3.795A pdb=" N ASP B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 624 removed outlier: 4.002A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 666 removed outlier: 4.058A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 431 Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 456 through 473 removed outlier: 3.874A pdb=" N MET C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 removed outlier: 4.407A pdb=" N VAL C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 505 Processing helix chain 'C' and resid 522 through 532 Processing helix chain 'C' and resid 533 through 538 removed outlier: 3.796A pdb=" N ARG C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 538' Processing helix chain 'C' and resid 548 through 575 Processing helix chain 'C' and resid 585 through 593 removed outlier: 3.795A pdb=" N ASP C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 624 removed outlier: 4.002A pdb=" N ALA C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 666 removed outlier: 4.058A pdb=" N ALA C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 431 Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 456 through 473 removed outlier: 3.874A pdb=" N MET D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 497 removed outlier: 4.407A pdb=" N VAL D 491 " --> pdb=" O GLY D 487 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 505 Processing helix chain 'D' and resid 522 through 532 Processing helix chain 'D' and resid 533 through 538 removed outlier: 3.796A pdb=" N ARG D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 538' Processing helix chain 'D' and resid 548 through 575 Processing helix chain 'D' and resid 585 through 593 removed outlier: 3.795A pdb=" N ASP D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 624 removed outlier: 4.002A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 666 removed outlier: 4.058A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE D 656 " --> pdb=" O TYR D 652 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1332 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: 0.74 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1964 1.34 - 1.46: 1484 1.46 - 1.57: 3272 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 6756 Sorted by residual: bond pdb=" C THR D 425 " pdb=" N PRO D 426 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.37e+00 bond pdb=" C THR C 425 " pdb=" N PRO C 426 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.37e+00 bond pdb=" C THR B 425 " pdb=" N PRO B 426 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.37e+00 bond pdb=" C THR A 425 " pdb=" N PRO A 426 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.37e+00 bond pdb=" CA ILE A 521 " pdb=" CB ILE A 521 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.05e-02 9.07e+03 8.77e-01 ... (remaining 6751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 8660 1.16 - 2.32: 436 2.32 - 3.49: 100 3.49 - 4.65: 20 4.65 - 5.81: 8 Bond angle restraints: 9224 Sorted by residual: angle pdb=" N PHE A 498 " pdb=" CA PHE A 498 " pdb=" C PHE A 498 " ideal model delta sigma weight residual 114.62 111.11 3.51 1.14e+00 7.69e-01 9.47e+00 angle pdb=" N PHE B 498 " pdb=" CA PHE B 498 " pdb=" C PHE B 498 " ideal model delta sigma weight residual 114.62 111.11 3.51 1.14e+00 7.69e-01 9.47e+00 angle pdb=" N PHE C 498 " pdb=" CA PHE C 498 " pdb=" C PHE C 498 " ideal model delta sigma weight residual 114.62 111.11 3.51 1.14e+00 7.69e-01 9.47e+00 angle pdb=" N PHE D 498 " pdb=" CA PHE D 498 " pdb=" C PHE D 498 " ideal model delta sigma weight residual 114.62 111.11 3.51 1.14e+00 7.69e-01 9.47e+00 angle pdb=" CA PHE C 498 " pdb=" C PHE C 498 " pdb=" N LEU C 499 " ideal model delta sigma weight residual 119.71 116.85 2.86 1.17e+00 7.31e-01 5.97e+00 ... (remaining 9219 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 10.01: 3108 10.01 - 20.02: 452 20.02 - 30.02: 184 30.02 - 40.03: 68 40.03 - 50.03: 32 Dihedral angle restraints: 3844 sinusoidal: 1292 harmonic: 2552 Sorted by residual: dihedral pdb=" CA PHE C 656 " pdb=" C PHE C 656 " pdb=" N GLY C 657 " pdb=" CA GLY C 657 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PHE D 656 " pdb=" C PHE D 656 " pdb=" N GLY D 657 " pdb=" CA GLY D 657 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PHE A 656 " pdb=" C PHE A 656 " pdb=" N GLY A 657 " pdb=" CA GLY A 657 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 3841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 744 0.036 - 0.071: 312 0.071 - 0.107: 56 0.107 - 0.142: 20 0.142 - 0.178: 4 Chirality restraints: 1136 Sorted by residual: chirality pdb=" CA THR C 425 " pdb=" N THR C 425 " pdb=" C THR C 425 " pdb=" CB THR C 425 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA THR D 425 " pdb=" N THR D 425 " pdb=" C THR D 425 " pdb=" CB THR D 425 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA THR B 425 " pdb=" N THR B 425 " pdb=" C THR B 425 " pdb=" CB THR B 425 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.89e-01 ... (remaining 1133 not shown) Planarity restraints: 1100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 616 " 0.010 2.00e-02 2.50e+03 7.61e-03 1.16e+00 pdb=" CG TYR C 616 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 616 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 616 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 616 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 616 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 616 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 616 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 616 " -0.010 2.00e-02 2.50e+03 7.61e-03 1.16e+00 pdb=" CG TYR B 616 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 616 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 616 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 616 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 616 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 616 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 616 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 616 " -0.010 2.00e-02 2.50e+03 7.61e-03 1.16e+00 pdb=" CG TYR A 616 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 616 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 616 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 616 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 616 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 616 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 616 " -0.002 2.00e-02 2.50e+03 ... (remaining 1097 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.50: 32 2.50 - 3.16: 5920 3.16 - 3.82: 12816 3.82 - 4.48: 15316 4.48 - 5.14: 25262 Nonbonded interactions: 59346 Sorted by model distance: nonbonded pdb=" CG LEU A 646 " pdb=" CE MET D 554 " model vdw 1.843 3.890 nonbonded pdb=" CE MET A 554 " pdb=" CG LEU B 646 " model vdw 1.843 3.890 nonbonded pdb=" CE MET B 554 " pdb=" CG LEU C 646 " model vdw 1.843 3.890 nonbonded pdb=" CE MET C 554 " pdb=" CG LEU D 646 " model vdw 1.844 3.890 nonbonded pdb=" CD2 LEU A 646 " pdb=" CE MET D 554 " model vdw 1.867 3.880 ... (remaining 59341 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 402 through 666) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.220 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 0.004 0.023 6756 Z= 0.170 Angle : 0.623 5.810 9224 Z= 0.347 Chirality : 0.041 0.178 1136 Planarity : 0.003 0.016 1100 Dihedral : 13.322 50.033 2188 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.25), residues: 836 helix: -1.49 (0.17), residues: 644 sheet: None (None), residues: 0 loop : -2.85 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 488 TYR 0.018 0.002 TYR C 616 PHE 0.011 0.001 PHE B 640 TRP 0.009 0.002 TRP D 585 HIS 0.002 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6756) covalent geometry : angle 0.62326 ( 9224) hydrogen bonds : bond 0.06344 ( 476) hydrogen bonds : angle 3.93856 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.160 Fit side-chains REVERT: A 610 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7589 (ttmt) REVERT: A 652 TYR cc_start: 0.8354 (t80) cc_final: 0.8068 (t80) REVERT: B 610 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7595 (ttmt) REVERT: B 652 TYR cc_start: 0.8359 (t80) cc_final: 0.8067 (t80) REVERT: C 610 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7593 (ttmt) REVERT: C 652 TYR cc_start: 0.8356 (t80) cc_final: 0.8067 (t80) REVERT: D 610 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7585 (ttmt) REVERT: D 652 TYR cc_start: 0.8355 (t80) cc_final: 0.8064 (t80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0703 time to fit residues: 15.0712 Evaluate side-chains 125 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 HIS A 587 HIS A 588 ASN B 562 HIS B 587 HIS B 588 ASN C 562 HIS C 587 HIS C 588 ASN D 562 HIS D 587 HIS D 588 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.181349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142481 restraints weight = 11662.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142297 restraints weight = 8021.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144168 restraints weight = 6640.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.144717 restraints weight = 5301.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.144676 restraints weight = 4781.075| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6756 Z= 0.143 Angle : 0.594 6.390 9224 Z= 0.299 Chirality : 0.041 0.154 1136 Planarity : 0.003 0.019 1100 Dihedral : 4.765 17.722 920 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.47 % Allowed : 20.99 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.28), residues: 836 helix: -0.48 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -2.18 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 541 TYR 0.014 0.002 TYR A 616 PHE 0.014 0.002 PHE C 617 TRP 0.006 0.001 TRP B 585 HIS 0.001 0.001 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6756) covalent geometry : angle 0.59357 ( 9224) hydrogen bonds : bond 0.03465 ( 476) hydrogen bonds : angle 4.23109 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.211 Fit side-chains REVERT: A 610 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7583 (ttmt) REVERT: B 610 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7419 (ttmt) REVERT: C 610 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7597 (ttmt) REVERT: D 610 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7589 (ttmt) outliers start: 16 outliers final: 8 residues processed: 163 average time/residue: 0.0571 time to fit residues: 12.5877 Evaluate side-chains 152 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 618 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 12 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 0.0040 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.180170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145239 restraints weight = 11521.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.141500 restraints weight = 9903.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143266 restraints weight = 8494.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.143994 restraints weight = 5866.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144481 restraints weight = 5077.896| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6756 Z= 0.154 Angle : 0.585 6.319 9224 Z= 0.298 Chirality : 0.041 0.153 1136 Planarity : 0.003 0.018 1100 Dihedral : 4.619 16.857 920 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.70 % Allowed : 25.93 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.29), residues: 836 helix: -0.15 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -1.99 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 531 TYR 0.012 0.002 TYR B 616 PHE 0.012 0.001 PHE D 640 TRP 0.005 0.001 TRP B 568 HIS 0.001 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6756) covalent geometry : angle 0.58465 ( 9224) hydrogen bonds : bond 0.03523 ( 476) hydrogen bonds : angle 4.17272 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.208 Fit side-chains REVERT: A 610 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7357 (ttmt) REVERT: A 652 TYR cc_start: 0.7940 (t80) cc_final: 0.7599 (t80) REVERT: B 610 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7364 (ttmt) REVERT: B 652 TYR cc_start: 0.7936 (t80) cc_final: 0.7598 (t80) REVERT: C 610 LYS cc_start: 0.7884 (mtmt) cc_final: 0.7361 (ttmt) REVERT: C 652 TYR cc_start: 0.7947 (t80) cc_final: 0.7599 (t80) REVERT: D 610 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7541 (ttmt) REVERT: D 652 TYR cc_start: 0.7938 (t80) cc_final: 0.7584 (t80) outliers start: 24 outliers final: 8 residues processed: 162 average time/residue: 0.0633 time to fit residues: 13.8944 Evaluate side-chains 150 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 618 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 58 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 14 optimal weight: 0.0050 chunk 71 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 53 optimal weight: 0.0770 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.183599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142793 restraints weight = 11654.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145629 restraints weight = 7243.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.147404 restraints weight = 5326.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.148387 restraints weight = 4419.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.148961 restraints weight = 3968.818| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6756 Z= 0.102 Angle : 0.538 6.354 9224 Z= 0.266 Chirality : 0.039 0.145 1136 Planarity : 0.003 0.019 1100 Dihedral : 4.172 15.384 920 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.71 % Allowed : 26.23 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.30), residues: 836 helix: 0.24 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.76 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 531 TYR 0.008 0.001 TYR D 542 PHE 0.008 0.001 PHE A 463 TRP 0.026 0.002 TRP C 585 HIS 0.001 0.000 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 6756) covalent geometry : angle 0.53770 ( 9224) hydrogen bonds : bond 0.03103 ( 476) hydrogen bonds : angle 3.95072 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.187 Fit side-chains REVERT: A 461 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6522 (pt) REVERT: A 610 LYS cc_start: 0.7959 (mtmt) cc_final: 0.7494 (ttmt) REVERT: A 652 TYR cc_start: 0.8114 (t80) cc_final: 0.7675 (t80) REVERT: B 461 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6533 (pt) REVERT: B 610 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7495 (ttmt) REVERT: B 652 TYR cc_start: 0.8121 (t80) cc_final: 0.7687 (t80) REVERT: C 461 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6530 (pt) REVERT: C 610 LYS cc_start: 0.7957 (mtmt) cc_final: 0.7495 (ttmt) REVERT: C 652 TYR cc_start: 0.8127 (t80) cc_final: 0.7691 (t80) REVERT: D 461 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6527 (pt) REVERT: D 610 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7490 (ttmt) REVERT: D 652 TYR cc_start: 0.8126 (t80) cc_final: 0.7694 (t80) outliers start: 37 outliers final: 21 residues processed: 192 average time/residue: 0.0589 time to fit residues: 15.4902 Evaluate side-chains 173 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 542 TYR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 542 TYR Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 623 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 0.0010 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.170501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.127591 restraints weight = 12373.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.130450 restraints weight = 7235.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132262 restraints weight = 5210.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133212 restraints weight = 4284.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133694 restraints weight = 3851.536| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6756 Z= 0.112 Angle : 0.560 6.595 9224 Z= 0.282 Chirality : 0.041 0.163 1136 Planarity : 0.003 0.018 1100 Dihedral : 4.137 14.817 920 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.86 % Allowed : 29.01 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.30), residues: 836 helix: 0.28 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.55 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 531 TYR 0.011 0.001 TYR A 542 PHE 0.009 0.001 PHE D 640 TRP 0.015 0.001 TRP D 585 HIS 0.001 0.000 HIS D 562 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6756) covalent geometry : angle 0.55998 ( 9224) hydrogen bonds : bond 0.03207 ( 476) hydrogen bonds : angle 3.95583 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.229 Fit side-chains REVERT: A 528 ARG cc_start: 0.8708 (mtt-85) cc_final: 0.8112 (mtp180) REVERT: A 610 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7436 (ttmt) REVERT: A 652 TYR cc_start: 0.8244 (t80) cc_final: 0.7786 (t80) REVERT: B 528 ARG cc_start: 0.8725 (mtt-85) cc_final: 0.8107 (mtp180) REVERT: B 610 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7432 (ttmt) REVERT: B 652 TYR cc_start: 0.8257 (t80) cc_final: 0.7799 (t80) REVERT: C 528 ARG cc_start: 0.8727 (mtt-85) cc_final: 0.8111 (mtp180) REVERT: C 610 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7433 (ttmt) REVERT: C 652 TYR cc_start: 0.8265 (t80) cc_final: 0.7800 (t80) REVERT: D 528 ARG cc_start: 0.8715 (mtt-85) cc_final: 0.8111 (mtp180) REVERT: D 610 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7433 (ttmt) REVERT: D 652 TYR cc_start: 0.8266 (t80) cc_final: 0.7810 (t80) outliers start: 25 outliers final: 21 residues processed: 156 average time/residue: 0.0659 time to fit residues: 13.8031 Evaluate side-chains 153 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 542 TYR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 542 TYR Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 623 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.169859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126351 restraints weight = 12403.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129305 restraints weight = 7137.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131135 restraints weight = 5094.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132122 restraints weight = 4184.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132649 restraints weight = 3761.912| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6756 Z= 0.119 Angle : 0.556 6.297 9224 Z= 0.281 Chirality : 0.041 0.146 1136 Planarity : 0.003 0.025 1100 Dihedral : 4.148 14.564 920 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.32 % Allowed : 28.09 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.29), residues: 836 helix: 0.33 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.42 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 541 TYR 0.009 0.001 TYR A 542 PHE 0.010 0.001 PHE D 463 TRP 0.013 0.001 TRP A 585 HIS 0.001 0.000 HIS D 485 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6756) covalent geometry : angle 0.55648 ( 9224) hydrogen bonds : bond 0.03262 ( 476) hydrogen bonds : angle 3.91615 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.170 Fit side-chains REVERT: A 461 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.6568 (pt) REVERT: A 528 ARG cc_start: 0.8774 (mtt-85) cc_final: 0.8266 (mtp180) REVERT: A 610 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7419 (ttmt) REVERT: A 652 TYR cc_start: 0.8297 (t80) cc_final: 0.7871 (t80) REVERT: B 461 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6566 (pt) REVERT: B 528 ARG cc_start: 0.8786 (mtt-85) cc_final: 0.8265 (mtp180) REVERT: B 610 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7416 (ttmt) REVERT: B 652 TYR cc_start: 0.8309 (t80) cc_final: 0.7881 (t80) REVERT: C 461 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6558 (pt) REVERT: C 528 ARG cc_start: 0.8783 (mtt-85) cc_final: 0.8267 (mtp180) REVERT: C 610 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7417 (ttmt) REVERT: C 652 TYR cc_start: 0.8317 (t80) cc_final: 0.7878 (t80) REVERT: D 461 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6558 (pt) REVERT: D 528 ARG cc_start: 0.8781 (mtt-85) cc_final: 0.8267 (mtp180) REVERT: D 610 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7412 (ttmt) REVERT: D 652 TYR cc_start: 0.8318 (t80) cc_final: 0.7872 (t80) outliers start: 28 outliers final: 20 residues processed: 156 average time/residue: 0.0505 time to fit residues: 10.9920 Evaluate side-chains 160 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 0.0030 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN B 592 GLN C 592 GLN D 592 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.171309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128137 restraints weight = 12111.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.131001 restraints weight = 7090.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.132770 restraints weight = 5118.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.133656 restraints weight = 4228.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134347 restraints weight = 3833.369| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6756 Z= 0.109 Angle : 0.579 9.851 9224 Z= 0.278 Chirality : 0.040 0.144 1136 Planarity : 0.003 0.025 1100 Dihedral : 4.090 14.694 920 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.09 % Allowed : 29.94 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.29), residues: 836 helix: 0.42 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.22 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 488 TYR 0.008 0.001 TYR B 542 PHE 0.009 0.001 PHE D 463 TRP 0.011 0.001 TRP A 585 HIS 0.001 0.000 HIS D 562 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6756) covalent geometry : angle 0.57900 ( 9224) hydrogen bonds : bond 0.03130 ( 476) hydrogen bonds : angle 3.87447 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.275 Fit side-chains REVERT: A 461 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6610 (pt) REVERT: A 528 ARG cc_start: 0.8647 (mtt-85) cc_final: 0.8218 (mtp180) REVERT: A 610 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7412 (ttmt) REVERT: A 652 TYR cc_start: 0.8273 (t80) cc_final: 0.7897 (t80) REVERT: B 461 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6614 (pt) REVERT: B 528 ARG cc_start: 0.8655 (mtt-85) cc_final: 0.8218 (mtp180) REVERT: B 610 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7407 (ttmt) REVERT: B 652 TYR cc_start: 0.8304 (t80) cc_final: 0.7947 (t80) REVERT: C 461 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6599 (pt) REVERT: C 528 ARG cc_start: 0.8646 (mtt-85) cc_final: 0.8220 (mtp180) REVERT: C 610 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7408 (ttmt) REVERT: C 652 TYR cc_start: 0.8313 (t80) cc_final: 0.7949 (t80) REVERT: D 461 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6597 (pt) REVERT: D 528 ARG cc_start: 0.8651 (mtt-85) cc_final: 0.8237 (mtp180) REVERT: D 610 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7407 (ttmt) REVERT: D 652 TYR cc_start: 0.8309 (t80) cc_final: 0.7957 (t80) outliers start: 20 outliers final: 16 residues processed: 171 average time/residue: 0.0572 time to fit residues: 13.7566 Evaluate side-chains 159 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 623 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.170817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.129663 restraints weight = 12327.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130796 restraints weight = 7345.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132333 restraints weight = 5693.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132289 restraints weight = 4880.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132465 restraints weight = 4515.385| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6756 Z= 0.112 Angle : 0.587 8.256 9224 Z= 0.286 Chirality : 0.041 0.163 1136 Planarity : 0.003 0.025 1100 Dihedral : 4.078 14.577 920 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.09 % Allowed : 33.18 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.29), residues: 836 helix: 0.51 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.12 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 531 TYR 0.007 0.001 TYR D 542 PHE 0.010 0.001 PHE D 463 TRP 0.010 0.001 TRP C 585 HIS 0.001 0.000 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6756) covalent geometry : angle 0.58712 ( 9224) hydrogen bonds : bond 0.03177 ( 476) hydrogen bonds : angle 3.86174 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.220 Fit side-chains REVERT: A 461 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6874 (pt) REVERT: A 528 ARG cc_start: 0.8765 (mtt-85) cc_final: 0.8174 (mtp180) REVERT: A 610 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7488 (ttmt) REVERT: A 652 TYR cc_start: 0.8319 (t80) cc_final: 0.8008 (t80) REVERT: B 461 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6888 (pt) REVERT: B 528 ARG cc_start: 0.8764 (mtt-85) cc_final: 0.8170 (mtp180) REVERT: B 610 LYS cc_start: 0.7769 (mtmt) cc_final: 0.7309 (ttmt) REVERT: B 652 TYR cc_start: 0.8349 (t80) cc_final: 0.8034 (t80) REVERT: C 461 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6876 (pt) REVERT: C 528 ARG cc_start: 0.8768 (mtt-85) cc_final: 0.8177 (mtp180) REVERT: C 610 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7468 (ttmt) REVERT: C 652 TYR cc_start: 0.8353 (t80) cc_final: 0.8038 (t80) REVERT: D 461 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6873 (pt) REVERT: D 528 ARG cc_start: 0.8788 (mtt-85) cc_final: 0.8210 (mtp180) REVERT: D 610 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7467 (ttmt) REVERT: D 652 TYR cc_start: 0.8366 (t80) cc_final: 0.8048 (t80) outliers start: 20 outliers final: 12 residues processed: 159 average time/residue: 0.0517 time to fit residues: 11.5555 Evaluate side-chains 159 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 623 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 87 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 27 optimal weight: 0.0050 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 84 optimal weight: 0.0060 chunk 22 optimal weight: 1.9990 overall best weight: 0.4410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.172407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128844 restraints weight = 12337.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131570 restraints weight = 7114.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.133195 restraints weight = 5167.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.133993 restraints weight = 4307.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.134541 restraints weight = 3923.168| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6756 Z= 0.103 Angle : 0.571 8.046 9224 Z= 0.279 Chirality : 0.040 0.156 1136 Planarity : 0.003 0.019 1100 Dihedral : 3.966 15.641 920 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.47 % Allowed : 32.87 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.30), residues: 836 helix: 0.65 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -0.99 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 528 TYR 0.007 0.001 TYR A 652 PHE 0.009 0.001 PHE D 463 TRP 0.010 0.001 TRP C 585 HIS 0.000 0.000 HIS C 402 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6756) covalent geometry : angle 0.57120 ( 9224) hydrogen bonds : bond 0.03042 ( 476) hydrogen bonds : angle 3.81940 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.185 Fit side-chains REVERT: A 461 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6630 (pt) REVERT: A 528 ARG cc_start: 0.8706 (mtt-85) cc_final: 0.8230 (mtp180) REVERT: A 610 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7373 (ttmt) REVERT: B 461 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6629 (pt) REVERT: B 528 ARG cc_start: 0.8714 (mtt-85) cc_final: 0.8229 (mtp180) REVERT: B 610 LYS cc_start: 0.7817 (mtmt) cc_final: 0.7364 (ttmt) REVERT: C 461 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6622 (pt) REVERT: C 528 ARG cc_start: 0.8705 (mtt-85) cc_final: 0.8232 (mtp180) REVERT: C 610 LYS cc_start: 0.7820 (mtmt) cc_final: 0.7365 (ttmt) REVERT: D 461 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6619 (pt) REVERT: D 528 ARG cc_start: 0.8709 (mtt-85) cc_final: 0.8216 (mtp180) REVERT: D 554 MET cc_start: 0.8257 (tpp) cc_final: 0.8041 (tpp) REVERT: D 610 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7369 (ttmt) outliers start: 16 outliers final: 12 residues processed: 150 average time/residue: 0.0511 time to fit residues: 10.7933 Evaluate side-chains 151 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 623 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.167794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125721 restraints weight = 12187.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126259 restraints weight = 8770.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128079 restraints weight = 6522.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128617 restraints weight = 4804.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128825 restraints weight = 4701.346| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6756 Z= 0.147 Angle : 0.629 8.351 9224 Z= 0.309 Chirality : 0.043 0.158 1136 Planarity : 0.003 0.016 1100 Dihedral : 4.292 17.133 920 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.93 % Allowed : 31.64 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.30), residues: 836 helix: 0.58 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -0.93 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 541 TYR 0.013 0.002 TYR D 420 PHE 0.012 0.001 PHE C 640 TRP 0.010 0.001 TRP B 585 HIS 0.001 0.001 HIS D 562 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6756) covalent geometry : angle 0.62887 ( 9224) hydrogen bonds : bond 0.03368 ( 476) hydrogen bonds : angle 3.96400 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.229 Fit side-chains REVERT: A 461 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6778 (pt) REVERT: A 528 ARG cc_start: 0.8773 (mtt-85) cc_final: 0.8223 (mtp180) REVERT: A 610 LYS cc_start: 0.7758 (mtmt) cc_final: 0.7277 (ttmt) REVERT: B 461 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6771 (pt) REVERT: B 528 ARG cc_start: 0.8790 (mtt-85) cc_final: 0.8226 (mtp180) REVERT: B 610 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7489 (ttmt) REVERT: C 461 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6765 (pt) REVERT: C 528 ARG cc_start: 0.8784 (mtt-85) cc_final: 0.8228 (mtp180) REVERT: C 610 LYS cc_start: 0.7975 (mtmt) cc_final: 0.7492 (ttmt) REVERT: D 461 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6755 (pt) REVERT: D 528 ARG cc_start: 0.8792 (mtt-85) cc_final: 0.8250 (mtp180) REVERT: D 610 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7493 (ttmt) outliers start: 19 outliers final: 15 residues processed: 158 average time/residue: 0.0549 time to fit residues: 12.2094 Evaluate side-chains 159 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 623 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 73 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.170317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127175 restraints weight = 11964.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129749 restraints weight = 7063.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131417 restraints weight = 5170.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132252 restraints weight = 4305.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132838 restraints weight = 3904.764| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6756 Z= 0.119 Angle : 0.599 7.812 9224 Z= 0.293 Chirality : 0.042 0.155 1136 Planarity : 0.003 0.016 1100 Dihedral : 4.209 17.746 920 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.09 % Allowed : 33.95 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.30), residues: 836 helix: 0.79 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -0.85 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 541 TYR 0.008 0.001 TYR D 542 PHE 0.025 0.002 PHE A 617 TRP 0.010 0.001 TRP C 585 HIS 0.000 0.000 HIS D 402 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6756) covalent geometry : angle 0.59864 ( 9224) hydrogen bonds : bond 0.03277 ( 476) hydrogen bonds : angle 3.91303 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1011.44 seconds wall clock time: 18 minutes 8.00 seconds (1088.00 seconds total)