Starting phenix.real_space_refine on Sun Aug 4 19:20:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/08_2024/8xw0_38725.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/08_2024/8xw0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/08_2024/8xw0_38725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/08_2024/8xw0_38725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/08_2024/8xw0_38725.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/08_2024/8xw0_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 Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 488": "OD1" <-> "OD2" Residue "B ASP 562": "OD1" <-> "OD2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 669": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 6.67, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 4.33 Conformation dependent library (CDL) restraints added in 1.9 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: 1.10 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: 3.49 Time building geometry restraints manager: 4.75 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: 99.62 - 106.51: 294 106.51 - 113.39: 6426 113.39 - 120.28: 4445 120.28 - 127.17: 4460 127.17 - 134.06: 125 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: 0.00 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: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.660 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.250 ------------------------------------------------------------------------------- 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= 0.290 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 *********************** 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 fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 1.239 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: 0.2379 time to fit residues: 51.8239 Evaluate side-chains 122 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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= 0.250 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 *********************** 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 fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.8828 (ttt) cc_final: 0.8447 (ttp) REVERT: B 180 GLN cc_start: 0.6839 (mt0) cc_final: 0.6604 (mt0) REVERT: B 631 MET cc_start: 0.8900 (mmm) cc_final: 0.8678 (tpp) REVERT: B 688 GLU cc_start: 0.7401 (mp0) cc_final: 0.7184 (mm-30) REVERT: A 21 MET cc_start: 0.7977 (mmp) cc_final: 0.7557 (mmp) REVERT: A 541 GLU cc_start: 0.8171 (pt0) cc_final: 0.7846 (pm20) outliers start: 11 outliers final: 4 residues processed: 147 average time/residue: 0.2163 time to fit residues: 47.1782 Evaluate side-chains 127 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 69 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 104 optimal weight: 0.0870 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 124 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1491 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= 0.188 Angle : 0.597 7.951 15750 Z= 0.322 Chirality : 0.043 0.198 1814 Planarity : 0.005 0.066 1918 Dihedral : 17.274 172.781 1697 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.74 % Allowed : 10.26 % 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 (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: -0.01 (0.24), residues: 1388 helix: 0.93 (0.18), residues: 906 sheet: -2.94 (0.78), residues: 34 loop : -1.67 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 PHE 0.056 0.002 PHE A 627 TYR 0.009 0.001 TYR A 458 ARG 0.003 0.000 ARG B 56 *********************** 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 149 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: B 180 GLN cc_start: 0.6838 (mt0) cc_final: 0.6513 (mt0) REVERT: B 562 ASP cc_start: 0.7937 (m-30) cc_final: 0.7681 (m-30) REVERT: B 631 MET cc_start: 0.8927 (mmm) cc_final: 0.8645 (tpp) REVERT: B 688 GLU cc_start: 0.7557 (mp0) cc_final: 0.7347 (mm-30) REVERT: A 541 GLU cc_start: 0.8169 (pt0) cc_final: 0.7865 (pm20) outliers start: 21 outliers final: 8 residues processed: 144 average time/residue: 0.2055 time to fit residues: 45.1943 Evaluate side-chains 126 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 357 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 chunk 125 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1701 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= 0.202 Angle : 0.598 9.014 15750 Z= 0.320 Chirality : 0.044 0.198 1814 Planarity : 0.005 0.059 1918 Dihedral : 16.407 179.497 1696 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.90 % Allowed : 12.00 % Favored : 86.09 % 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: 0.17 (0.24), residues: 1388 helix: 1.11 (0.18), residues: 902 sheet: -2.89 (0.77), residues: 34 loop : -1.67 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.005 0.001 HIS B 615 PHE 0.058 0.002 PHE A 627 TYR 0.009 0.001 TYR B 456 ARG 0.002 0.000 ARG B 56 *********************** 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 fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.8631 (ttt) cc_final: 0.8319 (ttt) REVERT: B 180 GLN cc_start: 0.6867 (mt0) cc_final: 0.6509 (mt0) REVERT: B 475 PHE cc_start: 0.9038 (m-80) cc_final: 0.8758 (m-80) REVERT: B 562 ASP cc_start: 0.7973 (m-30) cc_final: 0.7433 (m-30) REVERT: B 631 MET cc_start: 0.8885 (mmm) cc_final: 0.8683 (tpp) REVERT: A 21 MET cc_start: 0.8030 (mmp) cc_final: 0.7807 (mmp) REVERT: A 56 ARG cc_start: 0.8160 (tpm170) cc_final: 0.7925 (tpt170) REVERT: A 541 GLU cc_start: 0.8180 (pt0) cc_final: 0.7803 (pm20) outliers start: 23 outliers final: 17 residues processed: 148 average time/residue: 0.1949 time to fit residues: 43.4051 Evaluate side-chains 143 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 428 MET 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 159 ILE 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 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 75 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 99 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.0070 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN A 299 GLN A 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1865 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= 0.203 Angle : 0.590 7.907 15750 Z= 0.316 Chirality : 0.043 0.180 1814 Planarity : 0.005 0.052 1918 Dihedral : 15.670 164.844 1696 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.32 % Allowed : 13.99 % Favored : 83.69 % 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: 0.24 (0.24), residues: 1388 helix: 1.16 (0.18), residues: 902 sheet: -2.84 (0.76), residues: 34 loop : -1.65 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.005 0.001 HIS B 615 PHE 0.048 0.002 PHE A 627 TYR 0.010 0.001 TYR A 456 ARG 0.002 0.000 ARG B 56 *********************** 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 164 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.8674 (ttt) cc_final: 0.8343 (ttt) REVERT: B 180 GLN cc_start: 0.6912 (mt0) cc_final: 0.6559 (mt0) REVERT: B 465 PHE cc_start: 0.7160 (t80) cc_final: 0.6918 (t80) REVERT: B 562 ASP cc_start: 0.7989 (m-30) cc_final: 0.7518 (m-30) REVERT: A 21 MET cc_start: 0.7951 (mmp) cc_final: 0.7633 (mmp) REVERT: A 56 ARG cc_start: 0.8149 (tpm170) cc_final: 0.7716 (tpt170) REVERT: A 76 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8318 (tt) REVERT: A 113 ASP cc_start: 0.8770 (t0) cc_final: 0.8417 (t0) REVERT: A 541 GLU cc_start: 0.8243 (pt0) cc_final: 0.7873 (pm20) outliers start: 28 outliers final: 19 residues processed: 151 average time/residue: 0.2074 time to fit residues: 46.1413 Evaluate side-chains 149 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 296 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 409 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 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 378 MET 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 120 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 133 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 70 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2018 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= 0.193 Angle : 0.580 9.328 15750 Z= 0.310 Chirality : 0.043 0.161 1814 Planarity : 0.005 0.050 1918 Dihedral : 14.962 144.404 1696 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.32 % Allowed : 14.74 % Favored : 82.95 % 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: 1.19 (0.18), residues: 912 sheet: -2.75 (0.77), residues: 34 loop : -1.62 (0.31), residues: 442 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 0.033 0.001 PHE B 513 TYR 0.010 0.001 TYR A 456 ARG 0.001 0.000 ARG B 197 *********************** 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 159 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: B 76 LEU cc_start: 0.8532 (tt) cc_final: 0.8305 (tt) REVERT: B 139 MET cc_start: 0.8674 (ttt) cc_final: 0.8365 (ttt) REVERT: B 180 GLN cc_start: 0.6950 (mt0) cc_final: 0.6604 (mt0) REVERT: B 562 ASP cc_start: 0.8105 (m-30) cc_final: 0.7670 (m-30) REVERT: B 691 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6549 (ptm160) REVERT: A 56 ARG cc_start: 0.8137 (tpm170) cc_final: 0.7705 (tpt170) REVERT: A 76 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 541 GLU cc_start: 0.8259 (pt0) cc_final: 0.7854 (pm20) outliers start: 28 outliers final: 16 residues processed: 147 average time/residue: 0.2113 time to fit residues: 46.0275 Evaluate side-chains 141 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 388 THR Chi-restraints excluded: chain B residue 409 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 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 15 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.0000 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2094 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= 0.196 Angle : 0.581 8.811 15750 Z= 0.312 Chirality : 0.043 0.210 1814 Planarity : 0.005 0.047 1918 Dihedral : 14.621 145.367 1696 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.90 % Allowed : 15.15 % Favored : 82.95 % 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: 0.33 (0.24), residues: 1388 helix: 1.20 (0.18), residues: 914 sheet: -2.72 (0.77), residues: 34 loop : -1.62 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 PHE 0.039 0.002 PHE A 627 TYR 0.014 0.001 TYR A 572 ARG 0.002 0.000 ARG A 691 *********************** 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 154 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: B 76 LEU cc_start: 0.8540 (tt) cc_final: 0.8194 (tt) REVERT: B 139 MET cc_start: 0.8671 (ttt) cc_final: 0.8364 (ttt) REVERT: B 180 GLN cc_start: 0.6952 (mt0) cc_final: 0.6606 (mt0) REVERT: B 465 PHE cc_start: 0.7295 (t80) cc_final: 0.7001 (t80) REVERT: B 562 ASP cc_start: 0.8111 (m-30) cc_final: 0.7700 (m-30) REVERT: B 691 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6560 (ptm160) REVERT: A 56 ARG cc_start: 0.8135 (tpm170) cc_final: 0.7679 (tpt170) REVERT: A 76 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8290 (tt) REVERT: A 141 ASN cc_start: 0.7870 (t0) cc_final: 0.7286 (t0) REVERT: A 286 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7715 (pp20) REVERT: A 541 GLU cc_start: 0.8275 (pt0) cc_final: 0.7817 (pm20) outliers start: 23 outliers final: 15 residues processed: 143 average time/residue: 0.2178 time to fit residues: 46.3441 Evaluate side-chains 141 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain B residue 409 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 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 53 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 104 optimal weight: 0.2980 chunk 120 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2185 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= 0.184 Angle : 0.576 8.956 15750 Z= 0.308 Chirality : 0.043 0.197 1814 Planarity : 0.005 0.046 1918 Dihedral : 14.276 147.034 1696 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % 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: 0.27 (0.24), residues: 1388 helix: 1.18 (0.18), residues: 924 sheet: -2.69 (0.77), residues: 34 loop : -1.79 (0.31), residues: 430 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 0.030 0.001 PHE B 627 TYR 0.012 0.001 TYR A 572 ARG 0.001 0.000 ARG B 678 *********************** 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 147 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: B 76 LEU cc_start: 0.8541 (tt) cc_final: 0.8198 (tt) REVERT: B 139 MET cc_start: 0.8650 (ttt) cc_final: 0.8330 (ttt) REVERT: B 180 GLN cc_start: 0.6956 (mt0) cc_final: 0.6621 (mt0) REVERT: B 254 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7094 (mm-30) REVERT: B 286 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7571 (pp20) REVERT: B 465 PHE cc_start: 0.7372 (t80) cc_final: 0.7105 (t80) REVERT: B 562 ASP cc_start: 0.8116 (m-30) cc_final: 0.7701 (m-30) REVERT: B 691 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6526 (ptm160) REVERT: A 56 ARG cc_start: 0.8135 (tpm170) cc_final: 0.7705 (tpt170) REVERT: A 141 ASN cc_start: 0.7832 (t0) cc_final: 0.7264 (t0) REVERT: A 183 MET cc_start: 0.8376 (tpt) cc_final: 0.8035 (mmm) REVERT: A 286 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7715 (pp20) REVERT: A 514 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7576 (m-10) REVERT: A 541 GLU cc_start: 0.8275 (pt0) cc_final: 0.7809 (pm20) outliers start: 21 outliers final: 13 residues processed: 138 average time/residue: 0.2049 time to fit residues: 42.6361 Evaluate side-chains 140 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 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 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 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 127 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 131 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2184 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= 0.219 Angle : 0.598 9.561 15750 Z= 0.320 Chirality : 0.044 0.189 1814 Planarity : 0.005 0.046 1918 Dihedral : 14.152 149.864 1696 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.74 % Allowed : 16.47 % Favored : 81.79 % 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: 0.27 (0.24), residues: 1388 helix: 1.13 (0.18), residues: 930 sheet: -3.18 (0.71), residues: 30 loop : -1.68 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 613 HIS 0.005 0.001 HIS B 615 PHE 0.066 0.002 PHE B 627 TYR 0.021 0.001 TYR A 572 ARG 0.002 0.000 ARG B 450 *********************** 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 fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: B 76 LEU cc_start: 0.8563 (tt) cc_final: 0.8324 (tt) REVERT: B 139 MET cc_start: 0.8689 (ttt) cc_final: 0.8381 (ttt) REVERT: B 180 GLN cc_start: 0.6972 (mt0) cc_final: 0.6636 (mt0) REVERT: B 254 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7063 (mm-30) REVERT: B 286 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7679 (pp20) REVERT: B 562 ASP cc_start: 0.8086 (m-30) cc_final: 0.7684 (m-30) REVERT: B 691 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6661 (ptm160) REVERT: A 56 ARG cc_start: 0.8150 (tpm170) cc_final: 0.7771 (tpm170) REVERT: A 141 ASN cc_start: 0.7885 (t0) cc_final: 0.7342 (t0) REVERT: A 286 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7748 (pp20) REVERT: A 514 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7665 (m-10) REVERT: A 541 GLU cc_start: 0.8307 (pt0) cc_final: 0.7800 (pm20) outliers start: 21 outliers final: 15 residues processed: 139 average time/residue: 0.2092 time to fit residues: 43.1402 Evaluate side-chains 141 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 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 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 296 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 126 optimal weight: 0.0770 chunk 109 optimal weight: 0.0010 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.4344 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11608 Z= 0.172 Angle : 0.573 9.187 15750 Z= 0.305 Chirality : 0.042 0.174 1814 Planarity : 0.005 0.045 1918 Dihedral : 13.828 152.142 1696 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.49 % Allowed : 17.38 % Favored : 81.13 % 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: 0.38 (0.24), residues: 1388 helix: 1.30 (0.18), residues: 908 sheet: -3.01 (0.73), residues: 30 loop : -1.69 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 613 HIS 0.004 0.001 HIS A 617 PHE 0.049 0.001 PHE B 627 TYR 0.012 0.001 TYR A 572 ARG 0.001 0.000 ARG A 691 ********************** 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 151 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.236 Fit side-chains REVERT: B 76 LEU cc_start: 0.8535 (tt) cc_final: 0.8297 (tt) REVERT: B 139 MET cc_start: 0.8617 (ttt) cc_final: 0.8295 (ttt) REVERT: B 180 GLN cc_start: 0.6965 (mt0) cc_final: 0.6637 (mt0) REVERT: B 514 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.6908 (m-10) REVERT: B 562 ASP cc_start: 0.8149 (m-30) cc_final: 0.7724 (m-30) REVERT: B 691 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6447 (ptm160) REVERT: A 56 ARG cc_start: 0.8119 (tpm170) cc_final: 0.7683 (tpm170) REVERT: A 141 ASN cc_start: 0.7750 (t0) cc_final: 0.7231 (t0) REVERT: A 183 MET cc_start: 0.8322 (tpt) cc_final: 0.7998 (mmm) REVERT: A 514 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7674 (m-10) REVERT: A 541 GLU cc_start: 0.8295 (pt0) cc_final: 0.7788 (pm20) outliers start: 18 outliers final: 12 residues processed: 144 average time/residue: 0.2026 time to fit residues: 43.9810 Evaluate side-chains 142 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 514 PHE 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 296 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.0020 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 13 optimal weight: 0.0370 chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 overall best weight: 0.5268 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.167735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.133772 restraints weight = 13652.811| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.85 r_work: 0.3395 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2413 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= 0.181 Angle : 0.582 8.749 15750 Z= 0.309 Chirality : 0.043 0.178 1814 Planarity : 0.005 0.044 1918 Dihedral : 13.674 154.027 1690 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.41 % Allowed : 17.63 % 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 (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: 0.43 (0.24), residues: 1388 helix: 1.29 (0.18), residues: 918 sheet: -2.91 (0.74), residues: 30 loop : -1.65 (0.30), 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 0.051 0.002 PHE B 627 TYR 0.013 0.001 TYR B 246 ARG 0.001 0.000 ARG B 595 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.48 seconds wall clock time: 42 minutes 26.06 seconds (2546.06 seconds total)