Starting phenix.real_space_refine on Wed Sep 17 20:47:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xw0_38725/09_2025/8xw0_38725.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xw0_38725/09_2025/8xw0_38725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xw0_38725/09_2025/8xw0_38725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xw0_38725/09_2025/8xw0_38725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xw0_38725/09_2025/8xw0_38725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xw0_38725/09_2025/8xw0_38725.map" } resolution = 3.11 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= 0.004 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 40 5.16 5 C 7508 2.51 5 N 1792 2.21 5 O 1976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11320 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5577 Classifications: {'peptide': 696} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 663} Chain: "A" Number of atoms: 5577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5577 Classifications: {'peptide': 696} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 663} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Time building chain proxies: 2.76, per 1000 atoms: 0.24 Number of scatterers: 11320 At special positions: 0 Unit cell: (92.84, 140.315, 103.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 4 15.00 O 1976 8.00 N 1792 7.00 C 7508 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: 1.08 Conformation dependent library (CDL) restraints added in 554.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 69.3% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 2 through 28 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 38 through 43 Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 80 through 113 removed outlier: 3.726A pdb=" N HIS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Proline residue: B 104 - end of helix Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.755A pdb=" N ALA B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 118 through 123' Processing helix chain 'B' and resid 147 through 184 removed outlier: 3.854A pdb=" N ALA B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 233 through 261 Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.572A pdb=" N GLY B 272 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 302 Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 355 through 389 Proline residue: B 380 - end of helix removed outlier: 3.695A pdb=" N THR B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.593A pdb=" N ARG B 395 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'B' and resid 406 through 439 removed outlier: 3.588A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Proline residue: B 418 - end of helix Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 444 through 478 Processing helix chain 'B' and resid 485 through 523 removed outlier: 3.696A pdb=" N ILE B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Proline residue: B 499 - end of helix Processing helix chain 'B' and resid 523 through 530 Processing helix chain 'B' and resid 543 through 549 removed outlier: 3.882A pdb=" N ALA B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 578 through 601 removed outlier: 3.699A pdb=" N PHE B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 635 Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 646 through 664 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.757A pdb=" N GLU B 669 " --> pdb=" O TYR B 665 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS B 670 " --> pdb=" O GLY B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 670' Processing helix chain 'A' and resid 2 through 28 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 80 through 113 removed outlier: 3.727A pdb=" N HIS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Proline residue: A 104 - end of helix Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 118 through 123 removed outlier: 3.756A pdb=" N ALA A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 118 through 123' Processing helix chain 'A' and resid 147 through 184 removed outlier: 3.855A pdb=" N ALA A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 233 through 261 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.572A pdb=" N GLY A 272 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 355 through 389 Proline residue: A 380 - end of helix removed outlier: 3.695A pdb=" N THR A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.592A pdb=" N ARG A 395 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 406 through 439 removed outlier: 3.588A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Proline residue: A 418 - end of helix Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 444 through 478 Processing helix chain 'A' and resid 485 through 523 removed outlier: 3.696A pdb=" N ILE A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 543 through 549 removed outlier: 3.881A pdb=" N ALA A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 578 through 601 removed outlier: 3.700A pdb=" N PHE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 635 Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 646 through 664 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.757A pdb=" N GLU A 669 " --> pdb=" O TYR A 665 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS A 670 " --> pdb=" O GLY A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 670' Processing sheet with id=AA1, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.825A pdb=" N PHE B 314 " --> pdb=" O TYR B 225 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B 227 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL B 312 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL B 229 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 310 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 267 Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.825A pdb=" N PHE A 314 " --> pdb=" O TYR A 225 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER A 227 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL A 312 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL A 229 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA A 310 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267 686 hydrogen bonds defined for protein. 2022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1702 1.31 - 1.43: 3197 1.43 - 1.56: 6635 1.56 - 1.68: 8 1.68 - 1.81: 66 Bond restraints: 11608 Sorted by residual: bond pdb=" C38 P5S B 801 " pdb=" O37 P5S B 801 " ideal model delta sigma weight residual 1.345 1.407 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" C38 P5S A 801 " pdb=" O37 P5S A 801 " ideal model delta sigma weight residual 1.345 1.406 -0.061 2.00e-02 2.50e+03 9.40e+00 bond pdb=" C38 P5S B 802 " pdb=" O37 P5S B 802 " ideal model delta sigma weight residual 1.345 1.402 -0.057 2.00e-02 2.50e+03 8.10e+00 bond pdb=" C38 P5S A 802 " pdb=" O37 P5S A 802 " ideal model delta sigma weight residual 1.345 1.402 -0.057 2.00e-02 2.50e+03 8.06e+00 bond pdb=" C17 P5S A 802 " pdb=" O19 P5S A 802 " ideal model delta sigma weight residual 1.351 1.402 -0.051 2.00e-02 2.50e+03 6.54e+00 ... (remaining 11603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 15398 2.62 - 5.25: 272 5.25 - 7.87: 62 7.87 - 10.50: 12 10.50 - 13.12: 6 Bond angle restraints: 15750 Sorted by residual: angle pdb=" C LEU B 54 " pdb=" N THR B 55 " pdb=" CA THR B 55 " ideal model delta sigma weight residual 120.81 127.80 -6.99 1.63e+00 3.76e-01 1.84e+01 angle pdb=" C LEU A 54 " pdb=" N THR A 55 " pdb=" CA THR A 55 " ideal model delta sigma weight residual 120.81 127.79 -6.98 1.63e+00 3.76e-01 1.83e+01 angle pdb=" C LEU B 626 " pdb=" N PHE B 627 " pdb=" CA PHE B 627 " ideal model delta sigma weight residual 122.26 114.96 7.30 1.73e+00 3.34e-01 1.78e+01 angle pdb=" C LEU A 626 " pdb=" N PHE A 627 " pdb=" CA PHE A 627 " ideal model delta sigma weight residual 122.26 114.99 7.27 1.73e+00 3.34e-01 1.77e+01 angle pdb=" O13 P5S B 802 " pdb=" P12 P5S B 802 " pdb=" O15 P5S B 802 " ideal model delta sigma weight residual 121.25 109.04 12.21 3.00e+00 1.11e-01 1.66e+01 ... (remaining 15745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 6732 35.91 - 71.81: 165 71.81 - 107.72: 34 107.72 - 143.63: 15 143.63 - 179.54: 8 Dihedral angle restraints: 6954 sinusoidal: 2834 harmonic: 4120 Sorted by residual: dihedral pdb=" CA PHE B 627 " pdb=" C PHE B 627 " pdb=" N GLN B 628 " pdb=" CA GLN B 628 " ideal model delta harmonic sigma weight residual 180.00 154.26 25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PHE A 627 " pdb=" C PHE A 627 " pdb=" N GLN A 628 " pdb=" CA GLN A 628 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ARG B 691 " pdb=" C ARG B 691 " pdb=" N ALA B 692 " pdb=" CA ALA B 692 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 6951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1471 0.057 - 0.115: 299 0.115 - 0.172: 38 0.172 - 0.229: 3 0.229 - 0.286: 3 Chirality restraints: 1814 Sorted by residual: chirality pdb=" C2 P5S A 801 " pdb=" C1 P5S A 801 " pdb=" C3 P5S A 801 " pdb=" O37 P5S A 801 " both_signs ideal model delta sigma weight residual False 2.59 2.31 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C2 P5S B 801 " pdb=" C1 P5S B 801 " pdb=" C3 P5S B 801 " pdb=" O37 P5S B 801 " both_signs ideal model delta sigma weight residual False 2.59 2.34 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA PHE A 513 " pdb=" N PHE A 513 " pdb=" C PHE A 513 " pdb=" CB PHE A 513 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1811 not shown) Planarity restraints: 1918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 171 " 0.036 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR B 171 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR B 171 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 171 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 171 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 171 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 171 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 171 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 171 " 0.036 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR A 171 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR A 171 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 171 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 171 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 171 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 171 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 171 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 484 " 0.062 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO A 485 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " 0.052 5.00e-02 4.00e+02 ... (remaining 1915 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 194 2.68 - 3.24: 11524 3.24 - 3.79: 17752 3.79 - 4.35: 24272 4.35 - 4.90: 40247 Nonbonded interactions: 93989 Sorted by model distance: nonbonded pdb=" O LEU B 493 " pdb=" OG SER B 497 " model vdw 2.126 3.040 nonbonded pdb=" O LEU A 493 " pdb=" OG SER A 497 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR A 125 " pdb=" O SER A 127 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 125 " pdb=" O SER B 127 " model vdw 2.221 3.040 nonbonded pdb=" O THR A 473 " pdb=" OG1 THR A 477 " model vdw 2.232 3.040 ... (remaining 93984 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.005 0.062 11608 Z= 0.219 Angle : 0.907 13.120 15750 Z= 0.457 Chirality : 0.047 0.286 1814 Planarity : 0.006 0.094 1918 Dihedral : 19.549 179.535 4286 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.83 % Allowed : 0.83 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: -0.53 (0.24), residues: 1388 helix: 0.33 (0.18), residues: 906 sheet: -2.64 (0.97), residues: 30 loop : -1.45 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 29 TYR 0.069 0.002 TYR B 171 PHE 0.039 0.002 PHE B 513 TRP 0.034 0.002 TRP B 613 HIS 0.004 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00455 (11608) covalent geometry : angle 0.90713 (15750) hydrogen bonds : bond 0.14227 ( 686) hydrogen bonds : angle 6.74566 ( 2022) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.8452 (ttt) cc_final: 0.8217 (ttp) REVERT: B 180 GLN cc_start: 0.7058 (mt0) cc_final: 0.6762 (mt0) REVERT: B 242 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7904 (tptt) REVERT: B 465 PHE cc_start: 0.7502 (t80) cc_final: 0.7297 (t80) REVERT: A 29 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8217 (mtm180) REVERT: A 180 GLN cc_start: 0.7251 (mt0) cc_final: 0.7030 (mt0) REVERT: A 242 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7775 (tttp) REVERT: A 541 GLU cc_start: 0.8173 (pt0) cc_final: 0.7922 (pm20) outliers start: 10 outliers final: 4 residues processed: 152 average time/residue: 0.1187 time to fit residues: 25.9772 Evaluate side-chains 122 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 460 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN B 392 ASN A 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119986 restraints weight = 13532.626| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.02 r_work: 0.3230 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11608 Z= 0.158 Angle : 0.654 10.121 15750 Z= 0.351 Chirality : 0.044 0.199 1814 Planarity : 0.006 0.079 1918 Dihedral : 19.206 166.295 1710 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.99 % Allowed : 6.95 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: -0.25 (0.24), residues: 1388 helix: 0.61 (0.18), residues: 918 sheet: -3.14 (0.84), residues: 30 loop : -1.49 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 56 TYR 0.023 0.001 TYR B 171 PHE 0.060 0.002 PHE A 627 TRP 0.030 0.001 TRP A 613 HIS 0.005 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00347 (11608) covalent geometry : angle 0.65422 (15750) hydrogen bonds : bond 0.05165 ( 686) hydrogen bonds : angle 5.48800 ( 2022) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 GLN cc_start: 0.7699 (mt0) cc_final: 0.7361 (mt0) REVERT: B 612 MET cc_start: 0.8895 (ttt) cc_final: 0.8512 (ttt) REVERT: A 21 MET cc_start: 0.8277 (mmp) cc_final: 0.7950 (mmp) REVERT: A 180 GLN cc_start: 0.7897 (mt0) cc_final: 0.7598 (mt0) REVERT: A 541 GLU cc_start: 0.8286 (pt0) cc_final: 0.7854 (pm20) outliers start: 12 outliers final: 5 residues processed: 143 average time/residue: 0.1027 time to fit residues: 22.1997 Evaluate side-chains 120 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 286 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 35 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122014 restraints weight = 13559.508| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.02 r_work: 0.3257 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11608 Z= 0.138 Angle : 0.598 8.169 15750 Z= 0.322 Chirality : 0.043 0.187 1814 Planarity : 0.005 0.067 1918 Dihedral : 17.199 170.799 1697 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 1.32 % Allowed : 10.68 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.01 (0.24), residues: 1388 helix: 0.95 (0.18), residues: 906 sheet: -2.88 (0.78), residues: 34 loop : -1.67 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.009 0.001 TYR B 456 PHE 0.055 0.002 PHE A 627 TRP 0.024 0.001 TRP B 613 HIS 0.004 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00297 (11608) covalent geometry : angle 0.59792 (15750) hydrogen bonds : bond 0.04639 ( 686) hydrogen bonds : angle 5.16700 ( 2022) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.8985 (ttt) cc_final: 0.8782 (ttp) REVERT: B 180 GLN cc_start: 0.7725 (mt0) cc_final: 0.7298 (mt0) REVERT: B 562 ASP cc_start: 0.8337 (m-30) cc_final: 0.7847 (m-30) REVERT: A 56 ARG cc_start: 0.8382 (tpm170) cc_final: 0.8013 (tpt170) REVERT: A 180 GLN cc_start: 0.7924 (mt0) cc_final: 0.7668 (mt0) REVERT: A 541 GLU cc_start: 0.8274 (pt0) cc_final: 0.7849 (pm20) outliers start: 16 outliers final: 8 residues processed: 144 average time/residue: 0.0972 time to fit residues: 21.5047 Evaluate side-chains 130 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 286 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN B 392 ASN A 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.158199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122238 restraints weight = 13705.912| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.10 r_work: 0.3246 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11608 Z= 0.147 Angle : 0.603 8.809 15750 Z= 0.323 Chirality : 0.044 0.195 1814 Planarity : 0.005 0.058 1918 Dihedral : 16.432 175.971 1696 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.82 % Allowed : 12.33 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.16 (0.24), residues: 1388 helix: 1.10 (0.18), residues: 902 sheet: -2.89 (0.77), residues: 34 loop : -1.68 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 56 TYR 0.010 0.001 TYR B 456 PHE 0.058 0.002 PHE A 627 TRP 0.020 0.001 TRP A 613 HIS 0.005 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00331 (11608) covalent geometry : angle 0.60281 (15750) hydrogen bonds : bond 0.04665 ( 686) hydrogen bonds : angle 5.09698 ( 2022) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.9079 (ttt) cc_final: 0.8847 (ttp) REVERT: B 180 GLN cc_start: 0.7697 (mt0) cc_final: 0.7203 (mt0) REVERT: B 465 PHE cc_start: 0.7417 (t80) cc_final: 0.7206 (t80) REVERT: B 475 PHE cc_start: 0.9165 (m-80) cc_final: 0.8832 (m-80) REVERT: B 562 ASP cc_start: 0.8378 (m-30) cc_final: 0.7794 (m-30) REVERT: A 56 ARG cc_start: 0.8322 (tpm170) cc_final: 0.8017 (tpt170) REVERT: A 180 GLN cc_start: 0.7907 (mt0) cc_final: 0.7551 (mt0) REVERT: A 541 GLU cc_start: 0.8248 (pt0) cc_final: 0.7722 (pm20) outliers start: 22 outliers final: 15 residues processed: 143 average time/residue: 0.1009 time to fit residues: 21.8785 Evaluate side-chains 140 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 566 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 94 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 57 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.156661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121061 restraints weight = 13641.026| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.03 r_work: 0.3243 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11608 Z= 0.144 Angle : 0.597 9.233 15750 Z= 0.319 Chirality : 0.044 0.201 1814 Planarity : 0.005 0.052 1918 Dihedral : 15.768 174.954 1696 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.24 % Allowed : 13.66 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.23 (0.24), residues: 1388 helix: 1.17 (0.18), residues: 902 sheet: -2.82 (0.77), residues: 34 loop : -1.69 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 56 TYR 0.011 0.001 TYR A 456 PHE 0.046 0.002 PHE A 627 TRP 0.019 0.001 TRP A 613 HIS 0.005 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00323 (11608) covalent geometry : angle 0.59696 (15750) hydrogen bonds : bond 0.04583 ( 686) hydrogen bonds : angle 5.02187 ( 2022) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: B 76 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8539 (tt) REVERT: B 139 MET cc_start: 0.9026 (ttt) cc_final: 0.8805 (ttt) REVERT: B 180 GLN cc_start: 0.7796 (mt0) cc_final: 0.7325 (mt0) REVERT: B 562 ASP cc_start: 0.8368 (m-30) cc_final: 0.7813 (m-30) REVERT: B 691 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6998 (ptm160) REVERT: A 56 ARG cc_start: 0.8318 (tpm170) cc_final: 0.7780 (tpt170) REVERT: A 76 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8410 (tt) REVERT: A 113 ASP cc_start: 0.8790 (t0) cc_final: 0.8538 (t0) REVERT: A 145 LYS cc_start: 0.8137 (mttt) cc_final: 0.7935 (mttp) REVERT: A 488 ASP cc_start: 0.8181 (t70) cc_final: 0.7590 (t0) REVERT: A 541 GLU cc_start: 0.8354 (pt0) cc_final: 0.7876 (pm20) outliers start: 27 outliers final: 17 residues processed: 158 average time/residue: 0.1048 time to fit residues: 24.5826 Evaluate side-chains 150 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 95 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 129 optimal weight: 0.0670 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 137 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124811 restraints weight = 13623.580| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.10 r_work: 0.3278 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11608 Z= 0.131 Angle : 0.578 9.247 15750 Z= 0.308 Chirality : 0.043 0.164 1814 Planarity : 0.005 0.051 1918 Dihedral : 14.994 148.421 1696 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.24 % Allowed : 14.98 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.33 (0.24), residues: 1388 helix: 1.25 (0.18), residues: 900 sheet: -2.69 (0.79), residues: 34 loop : -1.64 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 691 TYR 0.010 0.001 TYR A 456 PHE 0.033 0.001 PHE B 513 TRP 0.018 0.001 TRP A 613 HIS 0.004 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00285 (11608) covalent geometry : angle 0.57780 (15750) hydrogen bonds : bond 0.04376 ( 686) hydrogen bonds : angle 4.94189 ( 2022) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.9061 (ttt) cc_final: 0.8828 (ttt) REVERT: B 180 GLN cc_start: 0.7749 (mt0) cc_final: 0.7262 (mt0) REVERT: B 461 VAL cc_start: 0.8509 (t) cc_final: 0.8296 (p) REVERT: B 465 PHE cc_start: 0.7486 (t80) cc_final: 0.7221 (t80) REVERT: B 475 PHE cc_start: 0.9071 (m-80) cc_final: 0.8808 (m-80) REVERT: B 562 ASP cc_start: 0.8403 (m-30) cc_final: 0.7914 (m-30) REVERT: A 56 ARG cc_start: 0.8281 (tpm170) cc_final: 0.7806 (tpt170) REVERT: A 76 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8407 (tt) REVERT: A 541 GLU cc_start: 0.8337 (pt0) cc_final: 0.7770 (pm20) REVERT: A 691 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7474 (ptt-90) outliers start: 27 outliers final: 13 residues processed: 151 average time/residue: 0.1022 time to fit residues: 23.2675 Evaluate side-chains 141 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 691 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 136 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119718 restraints weight = 13660.037| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.02 r_work: 0.3241 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11608 Z= 0.160 Angle : 0.603 8.877 15750 Z= 0.323 Chirality : 0.044 0.208 1814 Planarity : 0.005 0.046 1918 Dihedral : 14.643 144.272 1696 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.90 % Allowed : 15.81 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.28 (0.24), residues: 1388 helix: 1.15 (0.18), residues: 916 sheet: -2.74 (0.78), residues: 34 loop : -1.61 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 691 TYR 0.014 0.001 TYR A 572 PHE 0.033 0.002 PHE B 513 TRP 0.018 0.001 TRP A 613 HIS 0.006 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00367 (11608) covalent geometry : angle 0.60345 (15750) hydrogen bonds : bond 0.04646 ( 686) hydrogen bonds : angle 4.98644 ( 2022) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: B 76 LEU cc_start: 0.8646 (tt) cc_final: 0.8445 (tt) REVERT: B 139 MET cc_start: 0.9049 (ttt) cc_final: 0.8794 (ttp) REVERT: B 180 GLN cc_start: 0.7785 (mt0) cc_final: 0.7309 (mt0) REVERT: B 286 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7544 (pp20) REVERT: B 562 ASP cc_start: 0.8464 (m-30) cc_final: 0.8052 (m-30) REVERT: B 691 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7149 (ptm160) REVERT: A 56 ARG cc_start: 0.8295 (tpm170) cc_final: 0.7776 (tpt170) REVERT: A 76 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8423 (tt) REVERT: A 141 ASN cc_start: 0.8477 (t0) cc_final: 0.7908 (t0) REVERT: A 286 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7683 (pp20) REVERT: A 541 GLU cc_start: 0.8366 (pt0) cc_final: 0.7776 (pm20) outliers start: 23 outliers final: 14 residues processed: 143 average time/residue: 0.1074 time to fit residues: 22.9718 Evaluate side-chains 143 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 129 optimal weight: 0.0770 chunk 50 optimal weight: 3.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.164259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130084 restraints weight = 13694.129| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.85 r_work: 0.3349 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11608 Z= 0.140 Angle : 0.588 8.053 15750 Z= 0.315 Chirality : 0.043 0.202 1814 Planarity : 0.005 0.047 1918 Dihedral : 14.324 145.364 1696 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.74 % Allowed : 16.56 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.33 (0.24), residues: 1388 helix: 1.20 (0.18), residues: 916 sheet: -3.14 (0.73), residues: 30 loop : -1.60 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 450 TYR 0.018 0.001 TYR A 572 PHE 0.053 0.002 PHE A 627 TRP 0.018 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00312 (11608) covalent geometry : angle 0.58775 (15750) hydrogen bonds : bond 0.04477 ( 686) hydrogen bonds : angle 4.94759 ( 2022) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: B 180 GLN cc_start: 0.7909 (mt0) cc_final: 0.7494 (mt0) REVERT: B 286 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7582 (pp20) REVERT: B 465 PHE cc_start: 0.7794 (t80) cc_final: 0.7566 (t80) REVERT: B 480 ASP cc_start: 0.7674 (m-30) cc_final: 0.7447 (m-30) REVERT: B 488 ASP cc_start: 0.8142 (t70) cc_final: 0.7811 (t0) REVERT: B 562 ASP cc_start: 0.8481 (m-30) cc_final: 0.8058 (m-30) REVERT: B 691 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7054 (ptm160) REVERT: A 56 ARG cc_start: 0.8370 (tpm170) cc_final: 0.7862 (tpt170) REVERT: A 76 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8405 (tt) REVERT: A 141 ASN cc_start: 0.8476 (t0) cc_final: 0.7985 (t0) REVERT: A 286 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7782 (pp20) REVERT: A 514 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7897 (m-10) REVERT: A 541 GLU cc_start: 0.8399 (pt0) cc_final: 0.7879 (pm20) outliers start: 21 outliers final: 12 residues processed: 148 average time/residue: 0.1014 time to fit residues: 22.5809 Evaluate side-chains 144 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 49 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.164430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130200 restraints weight = 13739.534| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.89 r_work: 0.3349 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11608 Z= 0.138 Angle : 0.586 8.115 15750 Z= 0.313 Chirality : 0.043 0.193 1814 Planarity : 0.005 0.045 1918 Dihedral : 14.094 148.194 1696 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.57 % Allowed : 17.47 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.25 (0.24), residues: 1388 helix: 1.14 (0.18), residues: 930 sheet: -2.71 (0.77), residues: 34 loop : -1.78 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 450 TYR 0.015 0.001 TYR A 572 PHE 0.065 0.002 PHE B 627 TRP 0.018 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00307 (11608) covalent geometry : angle 0.58628 (15750) hydrogen bonds : bond 0.04431 ( 686) hydrogen bonds : angle 4.92342 ( 2022) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: B 180 GLN cc_start: 0.7879 (mt0) cc_final: 0.7462 (mt0) REVERT: B 254 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 286 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7662 (pp20) REVERT: B 562 ASP cc_start: 0.8482 (m-30) cc_final: 0.8109 (m-30) REVERT: B 691 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7078 (ptm160) REVERT: A 56 ARG cc_start: 0.8361 (tpm170) cc_final: 0.7849 (tpm170) REVERT: A 141 ASN cc_start: 0.8461 (t0) cc_final: 0.7995 (t0) REVERT: A 286 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7787 (pp20) REVERT: A 514 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: A 541 GLU cc_start: 0.8403 (pt0) cc_final: 0.7846 (pm20) outliers start: 19 outliers final: 11 residues processed: 140 average time/residue: 0.1066 time to fit residues: 22.3148 Evaluate side-chains 143 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 96 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.165701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131605 restraints weight = 13774.541| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.86 r_work: 0.3382 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11608 Z= 0.136 Angle : 0.590 8.827 15750 Z= 0.315 Chirality : 0.043 0.188 1814 Planarity : 0.005 0.045 1918 Dihedral : 13.937 150.166 1696 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.16 % Allowed : 18.13 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.31 (0.24), residues: 1388 helix: 1.19 (0.18), residues: 922 sheet: -3.15 (0.70), residues: 30 loop : -1.69 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 691 TYR 0.021 0.001 TYR A 572 PHE 0.056 0.002 PHE B 627 TRP 0.018 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00298 (11608) covalent geometry : angle 0.58983 (15750) hydrogen bonds : bond 0.04429 ( 686) hydrogen bonds : angle 4.91746 ( 2022) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: B 180 GLN cc_start: 0.7868 (mt0) cc_final: 0.7439 (mt0) REVERT: B 254 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 562 ASP cc_start: 0.8493 (m-30) cc_final: 0.8140 (m-30) REVERT: B 691 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7067 (ptm160) REVERT: A 56 ARG cc_start: 0.8362 (tpm170) cc_final: 0.7856 (tpm170) REVERT: A 141 ASN cc_start: 0.8436 (t0) cc_final: 0.7961 (t0) REVERT: A 514 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7957 (m-10) REVERT: A 541 GLU cc_start: 0.8412 (pt0) cc_final: 0.7831 (pm20) outliers start: 14 outliers final: 12 residues processed: 133 average time/residue: 0.1028 time to fit residues: 20.7172 Evaluate side-chains 140 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 66 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 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 = 0.3929 r_free = 0.3929 target = 0.165860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131684 restraints weight = 13867.854| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.87 r_work: 0.3367 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11608 Z= 0.139 Angle : 0.591 9.075 15750 Z= 0.316 Chirality : 0.043 0.189 1814 Planarity : 0.005 0.044 1918 Dihedral : 13.743 152.505 1690 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 1.32 % Allowed : 18.29 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.31 (0.24), residues: 1388 helix: 1.22 (0.18), residues: 920 sheet: -2.70 (0.76), residues: 34 loop : -1.77 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 450 TYR 0.018 0.001 TYR A 572 PHE 0.059 0.002 PHE B 465 TRP 0.018 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00307 (11608) covalent geometry : angle 0.59071 (15750) hydrogen bonds : bond 0.04428 ( 686) hydrogen bonds : angle 4.90521 ( 2022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3146.41 seconds wall clock time: 54 minutes 53.69 seconds (3293.69 seconds total)