Starting phenix.real_space_refine on Thu Jun 27 00:08:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/06_2024/8xw0_38725_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/06_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_38725/06_2024/8xw0_38725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/06_2024/8xw0_38725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/06_2024/8xw0_38725_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/06_2024/8xw0_38725_updated.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 6.28, per 1000 atoms: 0.55 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: 4.43 Conformation dependent library (CDL) restraints added in 1.8 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... running ksdssp... Secondary structure from input PDB file: 54 helices and 4 sheets defined 62.9% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'B' and resid 3 through 27 Processing helix chain 'B' and resid 31 through 37 Proline residue: B 35 - end of helix Processing helix chain 'B' and resid 39 through 42 No H-bonds generated for 'chain 'B' and resid 39 through 42' Processing helix chain 'B' and resid 58 through 66 removed outlier: 4.466A pdb=" N TRP B 61 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET B 62 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B 64 " --> pdb=" O TRP B 61 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 65 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 66 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 Processing helix chain 'B' and resid 79 through 112 removed outlier: 3.641A pdb=" N VAL B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) 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 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 147 through 183 removed outlier: 3.531A pdb=" N VAL B 174 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 182 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B 183 " --> pdb=" O GLN B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 216 through 219 No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 234 through 260 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 302 Processing helix chain 'B' and resid 318 through 325 removed outlier: 4.142A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 388 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 398 through 401 Processing helix chain 'B' and resid 407 through 440 Proline residue: B 418 - end of helix Proline residue: B 430 - end of helix removed outlier: 3.690A pdb=" N GLU B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 477 Processing helix chain 'B' and resid 486 through 522 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 524 through 529 Processing helix chain 'B' and resid 544 through 548 removed outlier: 3.807A pdb=" N TRP B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 544 through 548' Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 579 through 600 Processing helix chain 'B' and resid 613 through 637 removed outlier: 4.500A pdb=" N GLY B 636 " --> pdb=" O PHE B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 663 Proline residue: B 648 - end of helix Processing helix chain 'B' and resid 665 through 669 removed outlier: 3.675A pdb=" N GLU B 669 " --> pdb=" O GLY B 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 27 Processing helix chain 'A' and resid 31 through 37 Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 39 through 42 No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 58 through 66 removed outlier: 4.465A pdb=" N TRP A 61 " --> pdb=" O PRO A 58 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET A 62 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 64 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 65 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 66 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 76 Processing helix chain 'A' and resid 79 through 112 removed outlier: 3.641A pdb=" N VAL A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) 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 119 through 122 No H-bonds generated for 'chain 'A' and resid 119 through 122' Processing helix chain 'A' and resid 147 through 183 removed outlier: 3.532A pdb=" N VAL A 174 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 182 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 183 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 216 through 219 No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 234 through 260 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 302 Processing helix chain 'A' and resid 318 through 325 removed outlier: 4.142A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 388 Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 398 through 401 Processing helix chain 'A' and resid 407 through 440 Proline residue: A 418 - end of helix Proline residue: A 430 - end of helix removed outlier: 3.690A pdb=" N GLU A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 477 Processing helix chain 'A' and resid 486 through 522 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 524 through 529 Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.806A pdb=" N TRP A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 544 through 548' Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 579 through 600 Processing helix chain 'A' and resid 613 through 637 removed outlier: 4.500A pdb=" N GLY A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 663 Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.675A pdb=" N GLU A 669 " --> pdb=" O GLY A 666 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 337 through 340 removed outlier: 3.517A pdb=" N ARG B 226 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 265 through 267 Processing sheet with id= C, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.517A pdb=" N ARG A 226 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 265 through 267 618 hydrogen bonds defined for protein. 1638 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: 3.28 Time building geometry restraints manager: 4.87 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: 198 2.68 - 3.24: 11614 3.24 - 3.79: 17756 3.79 - 4.35: 24410 4.35 - 4.90: 40283 Nonbonded interactions: 94261 Sorted by model distance: nonbonded pdb=" O LEU B 493 " pdb=" OG SER B 497 " model vdw 2.126 2.440 nonbonded pdb=" O LEU A 493 " pdb=" OG SER A 497 " model vdw 2.126 2.440 nonbonded pdb=" OG1 THR A 125 " pdb=" O SER A 127 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR B 125 " pdb=" O SER B 127 " model vdw 2.221 2.440 nonbonded pdb=" O THR A 473 " pdb=" OG1 THR A 477 " model vdw 2.232 2.440 ... (remaining 94256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.390 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 31.150 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.670 ------------------------------------------------------------------------------- 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= 0.294 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 : 1.224 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: 0.2420 time to fit residues: 52.4858 Evaluate side-chains 122 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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: 3.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11608 Z= 0.265 Angle : 0.650 9.918 15750 Z= 0.351 Chirality : 0.044 0.189 1814 Planarity : 0.006 0.077 1918 Dihedral : 19.256 168.597 1710 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.91 % Allowed : 7.20 % Favored : 91.89 % 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: -0.65 (0.24), residues: 1388 helix: 0.32 (0.18), residues: 900 sheet: -2.90 (0.90), residues: 30 loop : -1.66 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 613 HIS 0.007 0.001 HIS B 615 PHE 0.057 0.002 PHE A 627 TYR 0.022 0.001 TYR B 171 ARG 0.003 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 144 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 GLN cc_start: 0.7075 (mt0) cc_final: 0.6794 (mt0) REVERT: B 612 MET cc_start: 0.8690 (ttt) cc_final: 0.8115 (ttt) REVERT: B 631 MET cc_start: 0.8916 (mmm) cc_final: 0.8663 (tpp) REVERT: B 688 GLU cc_start: 0.7410 (mp0) cc_final: 0.7189 (mm-30) REVERT: A 21 MET cc_start: 0.7994 (mmp) cc_final: 0.7566 (mmp) REVERT: A 180 GLN cc_start: 0.7164 (mt0) cc_final: 0.6962 (mt0) REVERT: A 183 MET cc_start: 0.8360 (tpt) cc_final: 0.8120 (tpp) REVERT: A 242 LYS cc_start: 0.8120 (tttm) cc_final: 0.7892 (tttp) REVERT: A 357 PHE cc_start: 0.7459 (m-80) cc_final: 0.7226 (m-80) REVERT: A 541 GLU cc_start: 0.8189 (pt0) cc_final: 0.7867 (pm20) outliers start: 11 outliers final: 6 residues processed: 142 average time/residue: 0.2180 time to fit residues: 45.4684 Evaluate side-chains 130 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 460 SER 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: 3.9990 chunk 104 optimal weight: 0.0670 chunk 85 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1264 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= 0.206 Angle : 0.583 8.109 15750 Z= 0.316 Chirality : 0.042 0.177 1814 Planarity : 0.006 0.064 1918 Dihedral : 17.246 175.083 1698 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 1.66 % Allowed : 9.52 % Favored : 88.82 % 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: -0.61 (0.24), residues: 1388 helix: 0.35 (0.18), residues: 904 sheet: -2.89 (0.85), residues: 30 loop : -1.67 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 613 HIS 0.005 0.001 HIS B 615 PHE 0.050 0.002 PHE A 627 TYR 0.010 0.001 TYR A 458 ARG 0.002 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 157 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.8304 (ttt) cc_final: 0.7853 (ttp) REVERT: B 180 GLN cc_start: 0.7030 (mt0) cc_final: 0.6815 (mt0) REVERT: B 254 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7048 (mm-30) REVERT: B 488 ASP cc_start: 0.8010 (t70) cc_final: 0.7657 (t0) REVERT: B 612 MET cc_start: 0.8678 (ttt) cc_final: 0.8098 (ttt) REVERT: B 631 MET cc_start: 0.8960 (mmm) cc_final: 0.8710 (tpp) REVERT: B 688 GLU cc_start: 0.7536 (mp0) cc_final: 0.7301 (mm-30) REVERT: A 183 MET cc_start: 0.8341 (tpt) cc_final: 0.8133 (tpp) REVERT: A 242 LYS cc_start: 0.8152 (tttm) cc_final: 0.7925 (tttp) REVERT: A 541 GLU cc_start: 0.8207 (pt0) cc_final: 0.7903 (pm20) REVERT: A 562 ASP cc_start: 0.8076 (m-30) cc_final: 0.7870 (m-30) outliers start: 20 outliers final: 10 residues processed: 152 average time/residue: 0.1942 time to fit residues: 45.1702 Evaluate side-chains 138 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 339 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 460 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.0370 chunk 94 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1544 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= 0.196 Angle : 0.573 8.432 15750 Z= 0.310 Chirality : 0.042 0.174 1814 Planarity : 0.005 0.056 1918 Dihedral : 16.244 175.419 1697 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.49 % Allowed : 11.26 % Favored : 87.25 % 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: -0.51 (0.24), residues: 1388 helix: 0.40 (0.18), residues: 914 sheet: -2.84 (0.83), residues: 30 loop : -1.60 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 613 HIS 0.005 0.001 HIS B 615 PHE 0.054 0.002 PHE B 627 TYR 0.009 0.001 TYR A 456 ARG 0.003 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 150 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.8286 (ttt) cc_final: 0.7828 (ttp) REVERT: B 180 GLN cc_start: 0.7069 (mt0) cc_final: 0.6835 (mt0) REVERT: B 254 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7048 (mm-30) REVERT: B 612 MET cc_start: 0.8708 (ttt) cc_final: 0.8171 (ttt) REVERT: B 631 MET cc_start: 0.8971 (mmm) cc_final: 0.8728 (tpp) REVERT: B 688 GLU cc_start: 0.7624 (mp0) cc_final: 0.7423 (mm-30) REVERT: A 21 MET cc_start: 0.8005 (mmp) cc_final: 0.7788 (mmp) REVERT: A 56 ARG cc_start: 0.8256 (tpm170) cc_final: 0.8054 (tpm170) REVERT: A 183 MET cc_start: 0.8352 (tpt) cc_final: 0.8083 (tpt) REVERT: A 242 LYS cc_start: 0.8183 (tttm) cc_final: 0.7956 (tttp) REVERT: A 541 GLU cc_start: 0.8236 (pt0) cc_final: 0.7890 (pm20) outliers start: 18 outliers final: 14 residues processed: 143 average time/residue: 0.2150 time to fit residues: 46.4948 Evaluate side-chains 144 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 339 THR 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 A residue 42 ILE Chi-restraints excluded: chain A residue 139 MET 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 339 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 99 optimal weight: 0.0170 chunk 55 optimal weight: 0.0050 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.4432 ------------------------------------------------------------------------------- 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 ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1754 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= 0.181 Angle : 0.553 7.487 15750 Z= 0.299 Chirality : 0.041 0.148 1814 Planarity : 0.005 0.054 1918 Dihedral : 15.367 148.923 1696 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 2.07 % Allowed : 12.00 % Favored : 85.93 % 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: -0.41 (0.24), residues: 1388 helix: 0.48 (0.18), residues: 914 sheet: -2.75 (0.84), residues: 30 loop : -1.57 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 613 HIS 0.004 0.001 HIS B 615 PHE 0.038 0.001 PHE B 627 TYR 0.009 0.001 TYR A 456 ARG 0.001 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 155 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.8235 (ttt) cc_final: 0.7794 (ttp) REVERT: B 157 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6674 (t80) REVERT: B 180 GLN cc_start: 0.7047 (mt0) cc_final: 0.6785 (mt0) REVERT: B 254 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7102 (mm-30) REVERT: B 488 ASP cc_start: 0.7853 (t70) cc_final: 0.7475 (t0) REVERT: B 612 MET cc_start: 0.8661 (ttt) cc_final: 0.8114 (ttt) REVERT: B 631 MET cc_start: 0.8918 (mmm) cc_final: 0.8680 (tpp) REVERT: A 56 ARG cc_start: 0.8238 (tpm170) cc_final: 0.7986 (tpm170) REVERT: A 183 MET cc_start: 0.8370 (tpt) cc_final: 0.8126 (tpt) REVERT: A 242 LYS cc_start: 0.8118 (tttm) cc_final: 0.7890 (tttp) REVERT: A 476 ASN cc_start: 0.8824 (m-40) cc_final: 0.8009 (m110) REVERT: A 498 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5881 (mp) REVERT: A 541 GLU cc_start: 0.8265 (pt0) cc_final: 0.7896 (pm20) outliers start: 25 outliers final: 15 residues processed: 148 average time/residue: 0.1993 time to fit residues: 44.3354 Evaluate side-chains 137 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 461 VAL 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 139 MET 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 339 THR Chi-restraints excluded: chain A residue 498 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1707 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= 0.292 Angle : 0.623 9.805 15750 Z= 0.335 Chirality : 0.044 0.176 1814 Planarity : 0.006 0.052 1918 Dihedral : 15.111 147.498 1696 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.07 % Allowed : 13.08 % Favored : 84.85 % 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: -0.46 (0.24), residues: 1388 helix: 0.42 (0.18), residues: 914 sheet: -2.86 (0.84), residues: 30 loop : -1.53 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 613 HIS 0.008 0.001 HIS B 615 PHE 0.068 0.002 PHE B 627 TYR 0.016 0.001 TYR B 456 ARG 0.003 0.000 ARG A 56 *********************** 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 157 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: B 139 MET cc_start: 0.8333 (ttt) cc_final: 0.7918 (ttp) REVERT: B 157 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6810 (t80) REVERT: B 180 GLN cc_start: 0.7120 (mt0) cc_final: 0.6909 (mt0) REVERT: B 254 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7094 (mm-30) REVERT: B 612 MET cc_start: 0.8788 (ttt) cc_final: 0.8261 (ttt) REVERT: B 691 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6934 (ptm160) REVERT: A 56 ARG cc_start: 0.8241 (tpm170) cc_final: 0.7881 (tpm170) REVERT: A 63 ARG cc_start: 0.6929 (mpt180) cc_final: 0.6579 (mmt180) REVERT: A 76 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 299 GLN cc_start: 0.6860 (mt0) cc_final: 0.6646 (mt0) REVERT: A 541 GLU cc_start: 0.8342 (pt0) cc_final: 0.7914 (pm20) outliers start: 25 outliers final: 17 residues processed: 150 average time/residue: 0.2177 time to fit residues: 48.1255 Evaluate side-chains 139 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 461 VAL 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 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 139 MET 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 296 GLU Chi-restraints excluded: chain A residue 339 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 133 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.0070 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1935 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= 0.176 Angle : 0.557 8.890 15750 Z= 0.299 Chirality : 0.041 0.192 1814 Planarity : 0.005 0.049 1918 Dihedral : 14.484 147.651 1696 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.74 % Allowed : 13.99 % Favored : 84.27 % 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: 0.54 (0.18), residues: 912 sheet: -2.74 (0.86), residues: 30 loop : -1.56 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 613 HIS 0.004 0.001 HIS A 617 PHE 0.051 0.001 PHE B 627 TYR 0.013 0.001 TYR A 572 ARG 0.002 0.000 ARG A 450 *********************** 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 150 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 157 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.6501 (t80) REVERT: B 180 GLN cc_start: 0.7055 (mt0) cc_final: 0.6703 (mt0) REVERT: B 254 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7123 (mm-30) REVERT: B 488 ASP cc_start: 0.7859 (t70) cc_final: 0.7489 (t0) REVERT: B 612 MET cc_start: 0.8689 (ttt) cc_final: 0.8165 (ttt) REVERT: B 691 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6492 (ptm160) REVERT: A 56 ARG cc_start: 0.8249 (tpm170) cc_final: 0.7842 (tpm170) REVERT: A 286 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7731 (pp20) REVERT: A 299 GLN cc_start: 0.6814 (mt0) cc_final: 0.6588 (mt0) REVERT: A 541 GLU cc_start: 0.8270 (pt0) cc_final: 0.7895 (pm20) REVERT: A 627 PHE cc_start: 0.4820 (m-80) cc_final: 0.4609 (m-80) outliers start: 21 outliers final: 12 residues processed: 142 average time/residue: 0.2113 time to fit residues: 44.2485 Evaluate side-chains 139 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 461 VAL 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 139 MET 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 296 GLU 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: 1.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 0.0050 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2009 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= 0.194 Angle : 0.560 8.238 15750 Z= 0.301 Chirality : 0.042 0.160 1814 Planarity : 0.005 0.046 1918 Dihedral : 14.266 149.171 1696 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.41 % Allowed : 14.57 % Favored : 84.02 % 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: -0.37 (0.24), residues: 1388 helix: 0.51 (0.18), residues: 922 sheet: -2.72 (0.85), residues: 30 loop : -1.60 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 613 HIS 0.005 0.001 HIS B 615 PHE 0.047 0.001 PHE B 627 TYR 0.010 0.001 TYR B 456 ARG 0.002 0.000 ARG A 56 *********************** 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 142 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 157 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6486 (t80) REVERT: B 180 GLN cc_start: 0.7139 (mt0) cc_final: 0.6746 (mt0) REVERT: B 254 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7114 (mm-30) REVERT: B 286 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7589 (pp20) REVERT: B 612 MET cc_start: 0.8701 (ttt) cc_final: 0.8180 (ttt) REVERT: B 691 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6597 (ptm160) REVERT: A 76 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8338 (tt) REVERT: A 286 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7736 (pp20) REVERT: A 299 GLN cc_start: 0.6825 (mt0) cc_final: 0.6599 (mt0) REVERT: A 476 ASN cc_start: 0.8697 (m-40) cc_final: 0.7783 (m110) REVERT: A 541 GLU cc_start: 0.8298 (pt0) cc_final: 0.7863 (pm20) outliers start: 17 outliers final: 11 residues processed: 136 average time/residue: 0.2162 time to fit residues: 43.5291 Evaluate side-chains 139 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 461 VAL 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 139 MET 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 296 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 74 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 81 optimal weight: 0.0170 chunk 131 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2134 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= 0.183 Angle : 0.561 8.009 15750 Z= 0.302 Chirality : 0.041 0.154 1814 Planarity : 0.005 0.046 1918 Dihedral : 14.040 150.799 1696 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 1.57 % Allowed : 14.82 % Favored : 83.61 % 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: 0.59 (0.18), residues: 914 sheet: -2.65 (0.85), residues: 30 loop : -1.53 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 613 HIS 0.004 0.001 HIS A 615 PHE 0.064 0.001 PHE B 627 TYR 0.015 0.001 TYR A 572 ARG 0.001 0.000 ARG B 558 *********************** 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 141 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 157 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.6400 (t80) REVERT: B 180 GLN cc_start: 0.7112 (mt0) cc_final: 0.6724 (mt0) REVERT: B 254 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7111 (mm-30) REVERT: B 286 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7658 (pp20) REVERT: B 612 MET cc_start: 0.8677 (ttt) cc_final: 0.8173 (ttt) REVERT: B 691 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6476 (ptm160) REVERT: A 76 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8327 (tt) REVERT: A 286 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7764 (pp20) REVERT: A 476 ASN cc_start: 0.8698 (m-40) cc_final: 0.7858 (m110) REVERT: A 541 GLU cc_start: 0.8304 (pt0) cc_final: 0.7828 (pm20) outliers start: 19 outliers final: 12 residues processed: 134 average time/residue: 0.2134 time to fit residues: 42.6212 Evaluate side-chains 135 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 566 LEU 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 139 MET 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 296 GLU Chi-restraints excluded: chain A residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.0770 chunk 62 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2297 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= 0.177 Angle : 0.553 8.689 15750 Z= 0.296 Chirality : 0.041 0.150 1814 Planarity : 0.005 0.044 1918 Dihedral : 13.772 153.502 1696 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 1.24 % Allowed : 15.07 % 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: -0.19 (0.24), residues: 1388 helix: 0.64 (0.18), residues: 914 sheet: -2.55 (0.86), residues: 30 loop : -1.48 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 613 HIS 0.004 0.001 HIS A 615 PHE 0.039 0.001 PHE B 627 TYR 0.012 0.001 TYR A 572 ARG 0.002 0.000 ARG B 197 ********************** 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 139 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: B 157 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.6318 (t80) REVERT: B 180 GLN cc_start: 0.7087 (mt0) cc_final: 0.6763 (mt0) REVERT: B 254 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7113 (mm-30) REVERT: B 612 MET cc_start: 0.8639 (ttt) cc_final: 0.8144 (ttt) REVERT: B 627 PHE cc_start: 0.5581 (m-80) cc_final: 0.5204 (m-10) REVERT: B 691 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6420 (ptm160) REVERT: A 76 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8175 (tt) REVERT: A 476 ASN cc_start: 0.8721 (m-40) cc_final: 0.7910 (m110) REVERT: A 541 GLU cc_start: 0.8330 (pt0) cc_final: 0.7831 (pm20) outliers start: 15 outliers final: 11 residues processed: 133 average time/residue: 0.2012 time to fit residues: 40.4807 Evaluate side-chains 133 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 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 691 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 0.0470 chunk 45 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 20 optimal weight: 0.0170 chunk 96 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 overall best weight: 0.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130529 restraints weight = 13227.356| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.96 r_work: 0.3390 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11608 Z= 0.162 Angle : 0.544 7.512 15750 Z= 0.289 Chirality : 0.040 0.146 1814 Planarity : 0.005 0.044 1918 Dihedral : 13.463 155.671 1690 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.08 % Allowed : 15.81 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.24), residues: 1388 helix: 0.75 (0.18), residues: 914 sheet: -2.38 (0.87), residues: 30 loop : -1.52 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 613 HIS 0.004 0.001 HIS A 615 PHE 0.029 0.001 PHE B 627 TYR 0.024 0.001 TYR B 246 ARG 0.002 0.000 ARG B 678 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2351.50 seconds wall clock time: 42 minutes 53.96 seconds (2573.96 seconds total)