Starting phenix.real_space_refine on Tue Feb 11 20:46:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cn0_30412/02_2025/7cn0_30412.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cn0_30412/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cn0_30412/02_2025/7cn0_30412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cn0_30412/02_2025/7cn0_30412.map" model { file = "/net/cci-nas-00/data/ceres_data/7cn0_30412/02_2025/7cn0_30412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cn0_30412/02_2025/7cn0_30412.cif" } resolution = 3.9 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= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} 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: 3.84, per 1000 atoms: 0.58 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: 1.74 Conformation dependent library (CDL) restraints added in 997.7 milliseconds 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: 0.57 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: 1.84 Time building geometry restraints manager: 2.01 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: 1.990 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.160 Find NCS groups from input model: 0.230 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- 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= 0.227 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (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 TRP 0.009 0.002 TRP D 585 HIS 0.002 0.001 HIS A 492 PHE 0.011 0.001 PHE B 640 TYR 0.018 0.002 TYR C 616 ARG 0.001 0.000 ARG D 488 *********************** 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 : 0.697 Fit side-chains REVERT: A 610 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7584 (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: 0.7590 (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: 0.7587 (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: 0.7579 (ttmt) REVERT: D 652 TYR cc_start: 0.8355 (t80) cc_final: 0.8063 (t80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1979 time to fit residues: 41.7147 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 : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN A 562 HIS A 576 GLN A 587 HIS A 588 ASN B 470 ASN B 562 HIS B 576 GLN B 587 HIS B 588 ASN C 562 HIS C 576 GLN C 587 HIS C 588 ASN D 470 ASN D 562 HIS D 576 GLN D 587 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.177930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.140701 restraints weight = 11546.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138265 restraints weight = 9367.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140343 restraints weight = 6828.592| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6756 Z= 0.294 Angle : 0.649 6.629 9224 Z= 0.331 Chirality : 0.043 0.153 1136 Planarity : 0.003 0.018 1100 Dihedral : 5.019 18.619 920 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.09 % Allowed : 20.37 % 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 (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: -1.72 (0.28), residues: 836 helix: -0.67 (0.19), residues: 648 sheet: None (None), residues: 0 loop : -2.31 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 568 HIS 0.002 0.001 HIS B 587 PHE 0.013 0.002 PHE A 640 TYR 0.018 0.002 TYR C 616 ARG 0.004 0.001 ARG A 531 *********************** 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 168 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.757 Fit side-chains REVERT: A 610 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7400 (ttmt) REVERT: B 610 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7406 (ttmt) REVERT: C 610 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7588 (ttmt) REVERT: D 610 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7592 (ttmt) outliers start: 20 outliers final: 12 residues processed: 156 average time/residue: 0.1801 time to fit residues: 37.4912 Evaluate side-chains 148 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 0.0040 chunk 47 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 overall best weight: 2.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 588 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.177405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.141649 restraints weight = 11635.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138967 restraints weight = 8858.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140373 restraints weight = 7866.363| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6756 Z= 0.301 Angle : 0.646 6.374 9224 Z= 0.332 Chirality : 0.043 0.153 1136 Planarity : 0.003 0.018 1100 Dihedral : 4.933 17.950 920 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.78 % Allowed : 26.08 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.29), residues: 836 helix: -0.39 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -2.02 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 568 HIS 0.002 0.001 HIS C 492 PHE 0.012 0.002 PHE D 640 TYR 0.015 0.002 TYR C 616 ARG 0.008 0.001 ARG D 531 *********************** 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 183 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.967 Fit side-chains REVERT: A 610 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7408 (ttmt) REVERT: A 652 TYR cc_start: 0.8051 (t80) cc_final: 0.7657 (t80) REVERT: B 610 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7414 (ttmt) REVERT: B 652 TYR cc_start: 0.8041 (t80) cc_final: 0.7648 (t80) REVERT: C 610 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7416 (ttmt) REVERT: C 652 TYR cc_start: 0.8053 (t80) cc_final: 0.7651 (t80) REVERT: D 610 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7643 (ttmt) REVERT: D 652 TYR cc_start: 0.8049 (t80) cc_final: 0.7657 (t80) outliers start: 31 outliers final: 15 residues processed: 168 average time/residue: 0.1842 time to fit residues: 41.5138 Evaluate side-chains 155 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 659 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.0050 chunk 55 optimal weight: 6.9990 chunk 46 optimal weight: 0.0980 chunk 44 optimal weight: 10.0000 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.181696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143373 restraints weight = 11798.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142859 restraints weight = 8471.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144808 restraints weight = 6591.999| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2274 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= 0.145 Angle : 0.552 6.327 9224 Z= 0.276 Chirality : 0.040 0.147 1136 Planarity : 0.004 0.042 1100 Dihedral : 4.349 15.580 920 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.32 % Allowed : 27.16 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.29), residues: 836 helix: 0.11 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.78 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 585 HIS 0.001 0.000 HIS C 402 PHE 0.007 0.001 PHE D 617 TYR 0.010 0.001 TYR D 542 ARG 0.011 0.001 ARG D 531 *********************** 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 185 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.693 Fit side-chains REVERT: A 415 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5944 (tt) REVERT: A 461 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6811 (pt) REVERT: A 610 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7564 (ttmt) REVERT: A 652 TYR cc_start: 0.8141 (t80) cc_final: 0.7705 (t80) REVERT: B 415 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5930 (tt) REVERT: B 461 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6817 (pt) REVERT: B 610 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7377 (ttmt) REVERT: B 652 TYR cc_start: 0.8133 (t80) cc_final: 0.7698 (t80) REVERT: C 415 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5946 (tt) REVERT: C 461 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6798 (pt) REVERT: C 610 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7561 (ttmt) REVERT: C 652 TYR cc_start: 0.8143 (t80) cc_final: 0.7701 (t80) REVERT: D 415 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5950 (tt) REVERT: D 461 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6804 (pt) REVERT: D 610 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7567 (ttmt) REVERT: D 652 TYR cc_start: 0.8139 (t80) cc_final: 0.7708 (t80) outliers start: 28 outliers final: 12 residues processed: 177 average time/residue: 0.1495 time to fit residues: 36.5555 Evaluate side-chains 165 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 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 B residue 415 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 C residue 415 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 D residue 415 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 59 optimal weight: 0.0770 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 0.0670 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 = 0.171000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128077 restraints weight = 11969.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130871 restraints weight = 6985.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132535 restraints weight = 5077.288| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6756 Z= 0.143 Angle : 0.555 6.530 9224 Z= 0.276 Chirality : 0.040 0.159 1136 Planarity : 0.003 0.019 1100 Dihedral : 4.158 15.250 920 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.78 % Allowed : 29.17 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.30), residues: 836 helix: 0.27 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.44 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 585 HIS 0.001 0.000 HIS D 485 PHE 0.009 0.001 PHE D 640 TYR 0.008 0.001 TYR D 542 ARG 0.008 0.001 ARG D 531 *********************** 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 179 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.687 Fit side-chains REVERT: A 415 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5822 (tt) REVERT: A 461 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6728 (pt) REVERT: A 528 ARG cc_start: 0.8626 (mtt-85) cc_final: 0.8165 (mtp180) REVERT: A 610 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7450 (ttmt) REVERT: A 652 TYR cc_start: 0.8192 (t80) cc_final: 0.7796 (t80) REVERT: B 415 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5825 (tt) REVERT: B 461 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6716 (pt) REVERT: B 528 ARG cc_start: 0.8626 (mtt-85) cc_final: 0.8166 (mtp180) REVERT: B 610 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7447 (ttmt) REVERT: B 652 TYR cc_start: 0.8193 (t80) cc_final: 0.7792 (t80) REVERT: C 415 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5827 (tt) REVERT: C 461 ILE cc_start: 0.6983 (OUTLIER) cc_final: 0.6711 (pt) REVERT: C 528 ARG cc_start: 0.8624 (mtt-85) cc_final: 0.8168 (mtp180) REVERT: C 610 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7440 (ttmt) REVERT: C 652 TYR cc_start: 0.8196 (t80) cc_final: 0.7794 (t80) REVERT: D 415 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5822 (tt) REVERT: D 461 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6727 (pt) REVERT: D 528 ARG cc_start: 0.8630 (mtt-85) cc_final: 0.8167 (mtp180) REVERT: D 610 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7446 (ttmt) REVERT: D 652 TYR cc_start: 0.8196 (t80) cc_final: 0.7798 (t80) outliers start: 31 outliers final: 12 residues processed: 172 average time/residue: 0.1522 time to fit residues: 35.9684 Evaluate side-chains 168 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 461 ILE 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 415 LEU Chi-restraints excluded: chain B residue 461 ILE 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 415 LEU Chi-restraints excluded: chain C residue 461 ILE 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 415 LEU Chi-restraints excluded: chain D residue 461 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.169555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126539 restraints weight = 12038.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129230 restraints weight = 7053.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.130945 restraints weight = 5108.681| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6756 Z= 0.181 Angle : 0.553 6.265 9224 Z= 0.279 Chirality : 0.041 0.148 1136 Planarity : 0.003 0.017 1100 Dihedral : 4.227 14.747 920 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.70 % Allowed : 30.09 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.30), residues: 836 helix: 0.30 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.32 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 585 HIS 0.001 0.000 HIS A 492 PHE 0.010 0.001 PHE A 640 TYR 0.008 0.001 TYR D 616 ARG 0.006 0.001 ARG D 531 *********************** 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 172 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.715 Fit side-chains REVERT: A 415 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5729 (tt) REVERT: A 461 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6528 (pt) REVERT: A 528 ARG cc_start: 0.8633 (mtt-85) cc_final: 0.8134 (mtp180) REVERT: A 610 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7444 (ttmt) REVERT: A 652 TYR cc_start: 0.8285 (t80) cc_final: 0.7900 (t80) REVERT: B 415 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5735 (tt) REVERT: B 461 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6521 (pt) REVERT: B 528 ARG cc_start: 0.8632 (mtt-85) cc_final: 0.8136 (mtp180) REVERT: B 610 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7444 (ttmt) REVERT: B 652 TYR cc_start: 0.8255 (t80) cc_final: 0.7851 (t80) REVERT: C 415 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5732 (tt) REVERT: C 461 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6516 (pt) REVERT: C 528 ARG cc_start: 0.8631 (mtt-85) cc_final: 0.8137 (mtp180) REVERT: C 610 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7439 (ttmt) REVERT: C 652 TYR cc_start: 0.8262 (t80) cc_final: 0.7848 (t80) REVERT: D 415 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5730 (tt) REVERT: D 461 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6527 (pt) REVERT: D 528 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8135 (mtp180) REVERT: D 610 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7441 (ttmt) REVERT: D 652 TYR cc_start: 0.8264 (t80) cc_final: 0.7855 (t80) outliers start: 24 outliers final: 15 residues processed: 164 average time/residue: 0.1807 time to fit residues: 39.3292 Evaluate side-chains 163 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 461 ILE 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 415 LEU Chi-restraints excluded: chain B residue 461 ILE 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 415 LEU Chi-restraints excluded: chain C residue 461 ILE 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 415 LEU Chi-restraints excluded: chain D residue 461 ILE 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 64 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.169359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126308 restraints weight = 12101.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129126 restraints weight = 7064.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130870 restraints weight = 5093.929| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6756 Z= 0.169 Angle : 0.558 6.293 9224 Z= 0.282 Chirality : 0.041 0.144 1136 Planarity : 0.003 0.023 1100 Dihedral : 4.185 14.601 920 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.78 % Allowed : 31.02 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.30), residues: 836 helix: 0.38 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.22 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 585 HIS 0.001 0.000 HIS A 492 PHE 0.013 0.001 PHE D 463 TYR 0.008 0.001 TYR A 542 ARG 0.005 0.001 ARG D 531 *********************** 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 163 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.757 Fit side-chains REVERT: A 415 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5747 (tt) REVERT: A 528 ARG cc_start: 0.8621 (mtt-85) cc_final: 0.8325 (mtp180) REVERT: A 610 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7453 (ttmt) REVERT: A 652 TYR cc_start: 0.8301 (t80) cc_final: 0.7951 (t80) REVERT: B 415 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5753 (tt) REVERT: B 528 ARG cc_start: 0.8623 (mtt-85) cc_final: 0.8325 (mtp180) REVERT: B 610 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7454 (ttmt) REVERT: B 652 TYR cc_start: 0.8267 (t80) cc_final: 0.7898 (t80) REVERT: C 415 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.5749 (tt) REVERT: C 528 ARG cc_start: 0.8623 (mtt-85) cc_final: 0.8326 (mtp180) REVERT: C 610 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7449 (ttmt) REVERT: C 652 TYR cc_start: 0.8276 (t80) cc_final: 0.7897 (t80) REVERT: D 415 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5752 (tt) REVERT: D 528 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.8329 (mtp180) REVERT: D 610 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7456 (ttmt) REVERT: D 652 TYR cc_start: 0.8274 (t80) cc_final: 0.7903 (t80) outliers start: 31 outliers final: 23 residues processed: 152 average time/residue: 0.1599 time to fit residues: 33.2198 Evaluate side-chains 159 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU 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 B residue 415 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 B residue 650 LEU Chi-restraints excluded: chain C residue 415 LEU 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 C residue 650 LEU Chi-restraints excluded: chain D residue 415 LEU 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 Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 7 optimal weight: 0.0770 chunk 46 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.173579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130278 restraints weight = 12084.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133160 restraints weight = 7114.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134751 restraints weight = 5158.137| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6756 Z= 0.135 Angle : 0.555 9.784 9224 Z= 0.271 Chirality : 0.040 0.143 1136 Planarity : 0.003 0.028 1100 Dihedral : 4.036 18.387 920 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.32 % Allowed : 30.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 836 helix: 0.58 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -1.16 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 585 HIS 0.001 0.000 HIS A 402 PHE 0.010 0.001 PHE D 463 TYR 0.008 0.001 TYR C 652 ARG 0.001 0.000 ARG D 531 *********************** 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 180 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.707 Fit side-chains REVERT: A 415 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5820 (tt) REVERT: A 461 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6616 (pt) REVERT: A 528 ARG cc_start: 0.8581 (mtt-85) cc_final: 0.8365 (mtp180) REVERT: A 554 MET cc_start: 0.8265 (tpp) cc_final: 0.8048 (tpp) REVERT: A 610 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7397 (ttmt) REVERT: A 652 TYR cc_start: 0.8235 (t80) cc_final: 0.8005 (t80) REVERT: B 415 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5823 (tt) REVERT: B 461 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6618 (pt) REVERT: B 528 ARG cc_start: 0.8579 (mtt-85) cc_final: 0.8365 (mtp180) REVERT: B 554 MET cc_start: 0.8265 (tpp) cc_final: 0.8047 (tpp) REVERT: B 610 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7395 (ttmt) REVERT: B 652 TYR cc_start: 0.8221 (t80) cc_final: 0.7999 (t80) REVERT: C 415 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5822 (tt) REVERT: C 461 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6611 (pt) REVERT: C 528 ARG cc_start: 0.8587 (mtt-85) cc_final: 0.8366 (mtp180) REVERT: C 554 MET cc_start: 0.8267 (tpp) cc_final: 0.8047 (tpp) REVERT: C 610 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7394 (ttmt) REVERT: C 652 TYR cc_start: 0.8226 (t80) cc_final: 0.8000 (t80) REVERT: D 415 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5824 (tt) REVERT: D 461 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6613 (pt) REVERT: D 528 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8349 (mtp180) REVERT: D 554 MET cc_start: 0.8273 (tpp) cc_final: 0.8053 (tpp) REVERT: D 610 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7396 (ttmt) REVERT: D 652 TYR cc_start: 0.8230 (t80) cc_final: 0.8003 (t80) outliers start: 28 outliers final: 16 residues processed: 172 average time/residue: 0.1525 time to fit residues: 36.1695 Evaluate side-chains 161 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 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 B residue 415 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 415 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 415 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 67 optimal weight: 0.0570 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.170086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126595 restraints weight = 12216.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129261 restraints weight = 7142.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130910 restraints weight = 5177.343| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3232 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= 0.150 Angle : 0.570 8.550 9224 Z= 0.278 Chirality : 0.041 0.169 1136 Planarity : 0.003 0.024 1100 Dihedral : 4.070 19.576 920 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.24 % Allowed : 30.25 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.30), residues: 836 helix: 0.66 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.06 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 585 HIS 0.001 0.000 HIS B 562 PHE 0.010 0.001 PHE D 463 TYR 0.014 0.001 TYR D 420 ARG 0.002 0.000 ARG D 531 *********************** 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 157 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.780 Fit side-chains REVERT: A 415 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5751 (tt) REVERT: A 461 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6575 (pt) REVERT: A 528 ARG cc_start: 0.8599 (mtt-85) cc_final: 0.8306 (mtp180) REVERT: A 610 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7461 (ttmt) REVERT: B 415 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.5742 (tt) REVERT: B 461 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6576 (pt) REVERT: B 528 ARG cc_start: 0.8606 (mtt-85) cc_final: 0.8305 (mtp180) REVERT: B 610 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7454 (ttmt) REVERT: C 415 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5741 (tt) REVERT: C 461 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6574 (pt) REVERT: C 528 ARG cc_start: 0.8608 (mtt-85) cc_final: 0.8303 (mtp180) REVERT: C 610 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7452 (ttmt) REVERT: D 415 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5750 (tt) REVERT: D 461 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6572 (pt) REVERT: D 528 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.8309 (mtp180) REVERT: D 554 MET cc_start: 0.8393 (tpp) cc_final: 0.8189 (tpp) REVERT: D 610 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7455 (ttmt) outliers start: 21 outliers final: 12 residues processed: 149 average time/residue: 0.1588 time to fit residues: 32.3696 Evaluate side-chains 152 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 461 ILE 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 B residue 415 LEU Chi-restraints excluded: chain B residue 461 ILE 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 415 LEU Chi-restraints excluded: chain C residue 461 ILE 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 415 LEU Chi-restraints excluded: chain D residue 461 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 71 optimal weight: 0.0010 chunk 49 optimal weight: 0.0010 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 76 optimal weight: 0.0270 overall best weight: 0.2250 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.174917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131855 restraints weight = 12202.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134655 restraints weight = 7153.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.136415 restraints weight = 5169.489| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6756 Z= 0.133 Angle : 0.584 8.584 9224 Z= 0.280 Chirality : 0.041 0.163 1136 Planarity : 0.003 0.020 1100 Dihedral : 4.025 20.531 920 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.55 % Allowed : 31.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.30), residues: 836 helix: 0.81 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -1.00 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 585 HIS 0.001 0.000 HIS C 402 PHE 0.009 0.001 PHE D 463 TYR 0.009 0.001 TYR D 652 ARG 0.002 0.000 ARG D 531 ********************** 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 162 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.763 Fit side-chains REVERT: A 415 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5874 (tt) REVERT: A 461 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6750 (pt) REVERT: A 528 ARG cc_start: 0.8568 (mtt-85) cc_final: 0.8278 (mtp180) REVERT: A 610 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7356 (ttmt) REVERT: B 415 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5875 (tt) REVERT: B 461 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6744 (pt) REVERT: B 528 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8277 (mtp180) REVERT: B 610 LYS cc_start: 0.7832 (mtmt) cc_final: 0.7357 (ttmt) REVERT: C 415 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5873 (tt) REVERT: C 461 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6741 (pt) REVERT: C 528 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.8277 (mtp180) REVERT: C 610 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7354 (ttmt) REVERT: D 415 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5871 (tt) REVERT: D 461 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6742 (pt) REVERT: D 528 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.8283 (mtp180) REVERT: D 610 LYS cc_start: 0.7829 (mtmt) cc_final: 0.7353 (ttmt) outliers start: 23 outliers final: 12 residues processed: 154 average time/residue: 0.1614 time to fit residues: 33.8088 Evaluate side-chains 154 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 461 ILE 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 B residue 415 LEU Chi-restraints excluded: chain B residue 461 ILE 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 415 LEU Chi-restraints excluded: chain C residue 461 ILE 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 415 LEU Chi-restraints excluded: chain D residue 461 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 86 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 75 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.0050 chunk 38 optimal weight: 0.7980 overall best weight: 0.3912 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.176825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133261 restraints weight = 11931.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135925 restraints weight = 7094.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137367 restraints weight = 5160.541| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6756 Z= 0.138 Angle : 0.584 8.414 9224 Z= 0.278 Chirality : 0.041 0.167 1136 Planarity : 0.003 0.019 1100 Dihedral : 4.024 20.480 920 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.70 % Allowed : 30.71 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.30), residues: 836 helix: 0.94 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -0.86 (0.53), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 585 HIS 0.001 0.000 HIS B 562 PHE 0.009 0.001 PHE A 463 TYR 0.016 0.001 TYR B 420 ARG 0.002 0.000 ARG A 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2198.21 seconds wall clock time: 40 minutes 28.27 seconds (2428.27 seconds total)