Starting phenix.real_space_refine on Tue Jul 29 10:30:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xw0_38725/07_2025/8xw0_38725.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xw0_38725/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xw0_38725/07_2025/8xw0_38725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xw0_38725/07_2025/8xw0_38725.map" model { file = "/net/cci-nas-00/data/ceres_data/8xw0_38725/07_2025/8xw0_38725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xw0_38725/07_2025/8xw0_38725.cif" } resolution = 3.11 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= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.58, per 1000 atoms: 0.67 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: 2.99 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.64 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: 3.80 Time building geometry restraints manager: 3.58 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.960 Set stop_for_unknowns flag: 0.010 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.180 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- 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 : 10.61 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 (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: -0.53 (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 TRP 0.034 0.002 TRP B 613 HIS 0.004 0.001 HIS B 615 PHE 0.039 0.002 PHE B 513 TYR 0.069 0.002 TYR B 171 ARG 0.011 0.001 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.14227 ( 686) hydrogen bonds : angle 6.74566 ( 2022) covalent geometry : bond 0.00455 (11608) covalent geometry : angle 0.90713 (15750) *********************** 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 : 1.323 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: 0.2650 time to fit residues: 58.2021 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 : 1.220 ------------------------------------------------------------------------------- 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 116 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.0040 chunk 125 optimal weight: 0.8980 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.154036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118401 restraints weight = 13451.767| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.02 r_work: 0.3210 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11608 Z= 0.170 Angle : 0.667 10.129 15750 Z= 0.356 Chirality : 0.045 0.194 1814 Planarity : 0.006 0.080 1918 Dihedral : 19.009 168.303 1710 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.91 % Allowed : 7.04 % 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 (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: -0.29 (0.24), residues: 1388 helix: 0.57 (0.18), residues: 918 sheet: -3.23 (0.82), residues: 30 loop : -1.50 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 613 HIS 0.006 0.001 HIS B 615 PHE 0.059 0.002 PHE A 627 TYR 0.025 0.001 TYR B 171 ARG 0.004 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.05233 ( 686) hydrogen bonds : angle 5.49732 ( 2022) covalent geometry : bond 0.00386 (11608) covalent geometry : angle 0.66689 (15750) *********************** 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 151 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.9132 (ttt) cc_final: 0.8813 (ttp) REVERT: B 180 GLN cc_start: 0.7718 (mt0) cc_final: 0.7396 (mt0) REVERT: B 631 MET cc_start: 0.8976 (mmm) cc_final: 0.8762 (tpp) REVERT: B 688 GLU cc_start: 0.7802 (mp0) cc_final: 0.7572 (mm-30) REVERT: A 21 MET cc_start: 0.8292 (mmp) cc_final: 0.7954 (mmp) REVERT: A 180 GLN cc_start: 0.7891 (mt0) cc_final: 0.7628 (mt0) REVERT: A 541 GLU cc_start: 0.8297 (pt0) cc_final: 0.7849 (pm20) outliers start: 11 outliers final: 4 residues processed: 147 average time/residue: 0.2197 time to fit residues: 48.2477 Evaluate side-chains 127 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 286 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.151492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116481 restraints weight = 13628.944| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.01 r_work: 0.3218 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11608 Z= 0.152 Angle : 0.612 8.068 15750 Z= 0.331 Chirality : 0.044 0.202 1814 Planarity : 0.005 0.066 1918 Dihedral : 17.439 173.577 1697 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 1.90 % Allowed : 10.35 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: -0.05 (0.24), residues: 1388 helix: 0.81 (0.18), residues: 918 sheet: -3.40 (0.76), residues: 30 loop : -1.51 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 613 HIS 0.005 0.001 HIS B 615 PHE 0.060 0.002 PHE A 627 TYR 0.011 0.001 TYR A 458 ARG 0.003 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 686) hydrogen bonds : angle 5.26292 ( 2022) covalent geometry : bond 0.00339 (11608) covalent geometry : angle 0.61224 (15750) *********************** 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 154 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: B 180 GLN cc_start: 0.7685 (mt0) cc_final: 0.7234 (mt0) REVERT: B 562 ASP cc_start: 0.8318 (m-30) cc_final: 0.7787 (m-30) REVERT: B 631 MET cc_start: 0.8940 (mmm) cc_final: 0.8723 (tpp) REVERT: B 688 GLU cc_start: 0.7953 (mp0) cc_final: 0.7692 (mm-30) REVERT: A 180 GLN cc_start: 0.7932 (mt0) cc_final: 0.7608 (mt0) REVERT: A 498 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6293 (mp) REVERT: A 541 GLU cc_start: 0.8280 (pt0) cc_final: 0.7817 (pm20) outliers start: 23 outliers final: 12 residues processed: 146 average time/residue: 0.2182 time to fit residues: 47.5823 Evaluate side-chains 136 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 B residue 677 CYS 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 357 PHE Chi-restraints excluded: chain A residue 498 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 107 optimal weight: 0.0040 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.156236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120749 restraints weight = 13565.753| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.02 r_work: 0.3240 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1669 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= 0.139 Angle : 0.596 9.100 15750 Z= 0.320 Chirality : 0.044 0.203 1814 Planarity : 0.005 0.057 1918 Dihedral : 16.435 177.423 1696 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.90 % Allowed : 13.08 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.14 (0.24), residues: 1388 helix: 1.06 (0.18), residues: 906 sheet: -2.98 (0.75), residues: 34 loop : -1.65 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 613 HIS 0.005 0.001 HIS B 615 PHE 0.061 0.002 PHE A 627 TYR 0.009 0.001 TYR B 456 ARG 0.002 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 686) hydrogen bonds : angle 5.10799 ( 2022) covalent geometry : bond 0.00305 (11608) covalent geometry : angle 0.59645 (15750) *********************** 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 158 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.8997 (ttt) cc_final: 0.8781 (ttt) REVERT: B 180 GLN cc_start: 0.7787 (mt0) cc_final: 0.7317 (mt0) REVERT: B 475 PHE cc_start: 0.9195 (m-80) cc_final: 0.8855 (m-80) REVERT: B 562 ASP cc_start: 0.8360 (m-30) cc_final: 0.7922 (m-30) REVERT: B 688 GLU cc_start: 0.8046 (mp0) cc_final: 0.7828 (mm-30) REVERT: A 56 ARG cc_start: 0.8343 (tpm170) cc_final: 0.8040 (tpt170) REVERT: A 498 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6208 (mp) REVERT: A 541 GLU cc_start: 0.8344 (pt0) cc_final: 0.7902 (pm20) outliers start: 23 outliers final: 15 residues processed: 149 average time/residue: 0.2535 time to fit residues: 57.6146 Evaluate side-chains 141 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 296 GLU Chi-restraints excluded: chain B residue 374 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 42 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 58 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.153242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117442 restraints weight = 13518.603| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.01 r_work: 0.3194 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11608 Z= 0.175 Angle : 0.620 8.154 15750 Z= 0.333 Chirality : 0.045 0.195 1814 Planarity : 0.005 0.054 1918 Dihedral : 15.849 156.560 1696 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.40 % Allowed : 14.82 % 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 (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: 0.15 (0.24), residues: 1388 helix: 1.02 (0.18), residues: 916 sheet: -3.45 (0.71), residues: 30 loop : -1.56 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 613 HIS 0.006 0.001 HIS B 615 PHE 0.057 0.002 PHE A 627 TYR 0.014 0.001 TYR B 456 ARG 0.002 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 686) hydrogen bonds : angle 5.14836 ( 2022) covalent geometry : bond 0.00408 (11608) covalent geometry : angle 0.62026 (15750) *********************** 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 161 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.9098 (ttt) cc_final: 0.8855 (ttp) REVERT: B 180 GLN cc_start: 0.7821 (mt0) cc_final: 0.7351 (mt0) REVERT: B 562 ASP cc_start: 0.8464 (m-30) cc_final: 0.8053 (m-30) REVERT: B 691 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7193 (ptm160) REVERT: A 56 ARG cc_start: 0.8324 (tpm170) cc_final: 0.7898 (tpm170) REVERT: A 76 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8427 (tt) REVERT: A 498 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6452 (mp) REVERT: A 541 GLU cc_start: 0.8396 (pt0) cc_final: 0.7885 (pm20) outliers start: 29 outliers final: 21 residues processed: 147 average time/residue: 0.2330 time to fit residues: 51.3726 Evaluate side-chains 151 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 157 TYR 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 428 MET 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 677 CYS 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 156 VAL 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 357 PHE Chi-restraints excluded: chain A residue 498 LEU 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 105 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 0.0370 chunk 121 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.156278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120744 restraints weight = 13761.631| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.03 r_work: 0.3243 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11608 Z= 0.138 Angle : 0.589 8.744 15750 Z= 0.314 Chirality : 0.043 0.156 1814 Planarity : 0.005 0.050 1918 Dihedral : 15.093 147.923 1696 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.15 % Allowed : 15.31 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.28 (0.24), residues: 1388 helix: 1.14 (0.18), residues: 912 sheet: -3.37 (0.71), residues: 30 loop : -1.53 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.004 0.001 HIS A 617 PHE 0.034 0.001 PHE B 513 TYR 0.009 0.001 TYR B 456 ARG 0.001 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 686) hydrogen bonds : angle 5.04244 ( 2022) covalent geometry : bond 0.00305 (11608) covalent geometry : angle 0.58903 (15750) *********************** 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 164 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: B 76 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8516 (tt) REVERT: B 139 MET cc_start: 0.9055 (ttt) cc_final: 0.8848 (ttt) REVERT: B 180 GLN cc_start: 0.7839 (mt0) cc_final: 0.7380 (mt0) REVERT: B 465 PHE cc_start: 0.7801 (t80) cc_final: 0.7524 (t80) REVERT: B 475 PHE cc_start: 0.9136 (m-80) cc_final: 0.8849 (m-80) REVERT: B 562 ASP cc_start: 0.8464 (m-30) cc_final: 0.8066 (m-30) REVERT: B 691 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7075 (ptm160) REVERT: A 56 ARG cc_start: 0.8338 (tpm170) cc_final: 0.7831 (tpt170) REVERT: A 76 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8361 (tt) REVERT: A 541 GLU cc_start: 0.8398 (pt0) cc_final: 0.7883 (pm20) outliers start: 26 outliers final: 14 residues processed: 154 average time/residue: 0.2167 time to fit residues: 49.9331 Evaluate side-chains 145 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU 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 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 357 PHE Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 22 optimal weight: 2.9990 chunk 129 optimal weight: 0.0070 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.163769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129470 restraints weight = 13858.601| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.88 r_work: 0.3343 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2043 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= 0.139 Angle : 0.589 8.963 15750 Z= 0.315 Chirality : 0.043 0.219 1814 Planarity : 0.005 0.048 1918 Dihedral : 14.778 147.791 1696 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.74 % Allowed : 15.98 % 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 (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: 0.30 (0.24), residues: 1388 helix: 1.15 (0.18), residues: 912 sheet: -3.31 (0.71), residues: 30 loop : -1.52 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 PHE 0.032 0.001 PHE B 513 TYR 0.012 0.001 TYR A 572 ARG 0.001 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 686) hydrogen bonds : angle 4.99564 ( 2022) covalent geometry : bond 0.00308 (11608) covalent geometry : angle 0.58902 (15750) *********************** 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 152 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: B 180 GLN cc_start: 0.7865 (mt0) cc_final: 0.7441 (mt0) REVERT: B 465 PHE cc_start: 0.7946 (t80) cc_final: 0.7659 (t80) REVERT: B 562 ASP cc_start: 0.8471 (m-30) cc_final: 0.8091 (m-30) REVERT: B 691 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7096 (ptm160) REVERT: A 56 ARG cc_start: 0.8367 (tpm170) cc_final: 0.7858 (tpt170) REVERT: A 76 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8406 (tt) REVERT: A 113 ASP cc_start: 0.8796 (t0) cc_final: 0.8531 (t0) REVERT: A 286 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7772 (pp20) REVERT: A 541 GLU cc_start: 0.8418 (pt0) cc_final: 0.7892 (pm20) outliers start: 21 outliers final: 12 residues processed: 141 average time/residue: 0.2271 time to fit residues: 47.5344 Evaluate side-chains 146 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 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 357 PHE 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 72 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.0170 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 74 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.165489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131338 restraints weight = 13735.634| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.86 r_work: 0.3380 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2186 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= 0.133 Angle : 0.584 9.719 15750 Z= 0.311 Chirality : 0.043 0.183 1814 Planarity : 0.005 0.045 1918 Dihedral : 14.313 149.736 1696 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.99 % Allowed : 16.72 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.34 (0.24), residues: 1388 helix: 1.22 (0.18), residues: 912 sheet: -3.24 (0.70), residues: 30 loop : -1.59 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.004 0.001 HIS A 617 PHE 0.051 0.001 PHE A 627 TYR 0.016 0.001 TYR A 572 ARG 0.002 0.000 ARG A 691 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 686) hydrogen bonds : angle 4.92687 ( 2022) covalent geometry : bond 0.00290 (11608) covalent geometry : angle 0.58422 (15750) *********************** 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 155 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: B 180 GLN cc_start: 0.7892 (mt0) cc_final: 0.7471 (mt0) REVERT: B 286 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: B 562 ASP cc_start: 0.8489 (m-30) cc_final: 0.8134 (m-30) REVERT: B 691 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7040 (ptm160) REVERT: A 56 ARG cc_start: 0.8365 (tpm170) cc_final: 0.7867 (tpt170) REVERT: A 76 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8341 (tt) REVERT: A 286 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7784 (pp20) REVERT: A 514 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7867 (m-10) REVERT: A 541 GLU cc_start: 0.8400 (pt0) cc_final: 0.7861 (pm20) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 0.2097 time to fit residues: 46.6060 Evaluate side-chains 141 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 357 PHE 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 116 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 95 optimal weight: 40.0000 chunk 117 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.164601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130461 restraints weight = 13787.170| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.86 r_work: 0.3352 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2228 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 : 0.587 9.358 15750 Z= 0.313 Chirality : 0.043 0.184 1814 Planarity : 0.005 0.046 1918 Dihedral : 14.158 151.674 1696 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.74 % Allowed : 17.55 % 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 (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 (0.24), residues: 1388 helix: 1.21 (0.18), residues: 918 sheet: -3.16 (0.70), residues: 30 loop : -1.59 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 613 HIS 0.004 0.001 HIS A 615 PHE 0.066 0.002 PHE B 627 TYR 0.015 0.001 TYR A 572 ARG 0.001 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 686) hydrogen bonds : angle 4.94669 ( 2022) covalent geometry : bond 0.00313 (11608) covalent geometry : angle 0.58712 (15750) *********************** 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 152 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 2.241 Fit side-chains revert: symmetry clash REVERT: B 180 GLN cc_start: 0.7923 (mt0) cc_final: 0.7507 (mt0) REVERT: B 254 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7233 (mm-30) REVERT: B 286 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7762 (pp20) REVERT: B 562 ASP cc_start: 0.8462 (m-30) cc_final: 0.8133 (m-30) REVERT: B 691 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7076 (ptm160) REVERT: A 56 ARG cc_start: 0.8366 (tpm170) cc_final: 0.7904 (tpm170) REVERT: A 141 ASN cc_start: 0.8491 (t0) cc_final: 0.7937 (t0) REVERT: A 286 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7783 (pp20) REVERT: A 541 GLU cc_start: 0.8418 (pt0) cc_final: 0.7880 (pm20) outliers start: 21 outliers final: 13 residues processed: 143 average time/residue: 0.2176 time to fit residues: 48.0338 Evaluate side-chains 144 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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 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 357 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 121 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 53 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.165088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131060 restraints weight = 13698.982| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.87 r_work: 0.3358 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2284 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 : 0.594 10.080 15750 Z= 0.314 Chirality : 0.043 0.255 1814 Planarity : 0.005 0.048 1918 Dihedral : 13.982 154.252 1696 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.49 % Allowed : 17.72 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % 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: 0.31 (0.24), residues: 1388 helix: 1.17 (0.18), residues: 926 sheet: -3.13 (0.70), residues: 30 loop : -1.65 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 PHE 0.059 0.001 PHE B 627 TYR 0.016 0.001 TYR A 572 ARG 0.002 0.000 ARG B 678 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 686) hydrogen bonds : angle 4.92351 ( 2022) covalent geometry : bond 0.00306 (11608) covalent geometry : angle 0.59355 (15750) ********************** 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 147 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: B 180 GLN cc_start: 0.7919 (mt0) cc_final: 0.7506 (mt0) REVERT: B 254 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7226 (mm-30) REVERT: B 562 ASP cc_start: 0.8456 (m-30) cc_final: 0.8130 (m-30) REVERT: B 691 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7063 (ptm160) REVERT: A 141 ASN cc_start: 0.8476 (t0) cc_final: 0.7928 (t0) REVERT: A 286 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7923 (pp20) REVERT: A 475 PHE cc_start: 0.9036 (m-80) cc_final: 0.8803 (m-80) REVERT: A 514 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7966 (m-10) REVERT: A 541 GLU cc_start: 0.8419 (pt0) cc_final: 0.7851 (pm20) REVERT: A 627 PHE cc_start: 0.4692 (m-80) cc_final: 0.4474 (m-80) outliers start: 18 outliers final: 14 residues processed: 139 average time/residue: 0.2670 time to fit residues: 56.5055 Evaluate side-chains 142 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 2.493 ------------------------------------------------------------------------------- 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 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 159 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 403 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 114 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.165687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131717 restraints weight = 13697.914| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.85 r_work: 0.3372 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11608 Z= 0.133 Angle : 0.588 8.669 15750 Z= 0.310 Chirality : 0.043 0.212 1814 Planarity : 0.005 0.046 1918 Dihedral : 13.782 156.916 1693 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.24 % Allowed : 18.38 % 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 (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: 0.36 (0.24), residues: 1388 helix: 1.24 (0.18), residues: 920 sheet: -3.08 (0.71), residues: 30 loop : -1.67 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 PHE 0.054 0.001 PHE B 627 TYR 0.015 0.001 TYR A 246 ARG 0.001 0.000 ARG B 595 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 686) hydrogen bonds : angle 4.90217 ( 2022) covalent geometry : bond 0.00293 (11608) covalent geometry : angle 0.58770 (15750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6444.80 seconds wall clock time: 113 minutes 9.42 seconds (6789.42 seconds total)