Starting phenix.real_space_refine on Sat Jul 20 15:12:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/07_2024/8xw0_38725.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/07_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_38725/07_2024/8xw0_38725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/07_2024/8xw0_38725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/07_2024/8xw0_38725.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw0_38725/07_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-5388/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: 6.79, per 1000 atoms: 0.60 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: 4.54 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: 1.00 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: 3.45 Time building geometry restraints manager: 4.99 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 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 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 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: 1.060 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.410 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- 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 : 1.272 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: 0.2458 time to fit residues: 53.4996 Evaluate side-chains 122 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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: 6.9990 chunk 104 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7740 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11608 Z= 0.213 Angle : 0.635 10.105 15750 Z= 0.338 Chirality : 0.044 0.193 1814 Planarity : 0.006 0.082 1918 Dihedral : 19.165 166.099 1710 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 0.91 % Allowed : 7.12 % Favored : 91.97 % 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: -0.22 (0.24), residues: 1388 helix: 0.61 (0.18), residues: 918 sheet: -3.08 (0.85), residues: 30 loop : -1.44 (0.33), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 PHE 0.060 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 146 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 GLN cc_start: 0.6799 (mt0) cc_final: 0.6561 (mt0) REVERT: B 488 ASP cc_start: 0.8117 (t70) cc_final: 0.7716 (t0) REVERT: B 612 MET cc_start: 0.8671 (ttt) cc_final: 0.8268 (ttt) REVERT: B 631 MET cc_start: 0.8927 (mmm) cc_final: 0.8626 (tpp) REVERT: B 688 GLU cc_start: 0.7384 (mp0) cc_final: 0.7174 (mm-30) REVERT: A 21 MET cc_start: 0.7962 (mmp) cc_final: 0.7559 (mmp) REVERT: A 180 GLN cc_start: 0.6978 (mt0) cc_final: 0.6753 (mt0) REVERT: A 183 MET cc_start: 0.8285 (tpt) cc_final: 0.8072 (tpp) REVERT: A 242 LYS cc_start: 0.8113 (tttm) cc_final: 0.7888 (tttp) REVERT: A 541 GLU cc_start: 0.8151 (pt0) cc_final: 0.7915 (pm20) outliers start: 11 outliers final: 6 residues processed: 143 average time/residue: 0.1998 time to fit residues: 42.9058 Evaluate side-chains 124 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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: 0.7731 moved from start: 0.1386 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= 0.199 Angle : 0.587 8.138 15750 Z= 0.315 Chirality : 0.043 0.194 1814 Planarity : 0.005 0.066 1918 Dihedral : 17.280 170.001 1698 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 1.99 % Allowed : 10.10 % Favored : 87.91 % 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: 0.06 (0.24), residues: 1388 helix: 0.97 (0.18), residues: 906 sheet: -2.84 (0.78), residues: 34 loop : -1.62 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 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 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 151 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.8170 (ttt) cc_final: 0.7918 (ttt) REVERT: B 180 GLN cc_start: 0.6827 (mt0) cc_final: 0.6501 (mt0) REVERT: B 475 PHE cc_start: 0.9011 (m-80) cc_final: 0.8718 (m-80) REVERT: B 562 ASP cc_start: 0.7915 (m-30) cc_final: 0.7413 (m-30) REVERT: B 631 MET cc_start: 0.8879 (mmm) cc_final: 0.8654 (tpp) REVERT: B 688 GLU cc_start: 0.7537 (mp0) cc_final: 0.7319 (mm-30) REVERT: A 180 GLN cc_start: 0.7040 (mt0) cc_final: 0.6822 (mt0) REVERT: A 242 LYS cc_start: 0.8164 (tttm) cc_final: 0.7933 (tttp) REVERT: A 541 GLU cc_start: 0.8172 (pt0) cc_final: 0.7800 (pm20) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 0.2021 time to fit residues: 44.9371 Evaluate side-chains 134 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 339 THR 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 184 SER 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: 0.6980 chunk 94 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN ** 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: 0.7738 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11608 Z= 0.213 Angle : 0.593 9.063 15750 Z= 0.317 Chirality : 0.043 0.204 1814 Planarity : 0.005 0.059 1918 Dihedral : 16.420 176.035 1697 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.57 % Allowed : 12.17 % Favored : 86.26 % 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: 1.09 (0.18), residues: 906 sheet: -2.85 (0.76), residues: 34 loop : -1.61 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 613 HIS 0.005 0.001 HIS B 615 PHE 0.060 0.002 PHE A 627 TYR 0.010 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 143 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: B 63 ARG cc_start: 0.6392 (mmt180) cc_final: 0.6079 (mpt180) REVERT: B 139 MET cc_start: 0.8165 (ttt) cc_final: 0.7910 (ttt) REVERT: B 180 GLN cc_start: 0.6898 (mt0) cc_final: 0.6542 (mt0) REVERT: B 562 ASP cc_start: 0.7968 (m-30) cc_final: 0.7422 (m-30) REVERT: A 21 MET cc_start: 0.8032 (mmp) cc_final: 0.7797 (mmp) REVERT: A 56 ARG cc_start: 0.8271 (tpm170) cc_final: 0.8003 (tpm170) REVERT: A 63 ARG cc_start: 0.6484 (mmt180) cc_final: 0.6156 (mmt180) REVERT: A 180 GLN cc_start: 0.7061 (mt0) cc_final: 0.6773 (mt0) REVERT: A 541 GLU cc_start: 0.8248 (pt0) cc_final: 0.7885 (pm20) outliers start: 19 outliers final: 17 residues processed: 136 average time/residue: 0.2100 time to fit residues: 42.8055 Evaluate side-chains 139 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 460 SER 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 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 339 THR Chi-restraints excluded: chain A residue 566 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.0870 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1708 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= 0.206 Angle : 0.584 10.047 15750 Z= 0.311 Chirality : 0.043 0.183 1814 Planarity : 0.005 0.052 1918 Dihedral : 15.722 174.846 1696 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.65 % Allowed : 12.83 % Favored : 84.52 % 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: 1.17 (0.18), residues: 906 sheet: -2.80 (0.75), residues: 34 loop : -1.61 (0.32), residues: 448 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 0.049 0.002 PHE A 627 TYR 0.010 0.001 TYR A 456 ARG 0.002 0.000 ARG A 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 160 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: B 63 ARG cc_start: 0.6487 (mmt180) cc_final: 0.6277 (mpt180) REVERT: B 139 MET cc_start: 0.8134 (ttt) cc_final: 0.7913 (ttt) REVERT: B 180 GLN cc_start: 0.6919 (mt0) cc_final: 0.6568 (mt0) REVERT: B 475 PHE cc_start: 0.8964 (m-80) cc_final: 0.8727 (m-80) REVERT: B 562 ASP cc_start: 0.8052 (m-30) cc_final: 0.7613 (m-30) REVERT: A 21 MET cc_start: 0.7952 (mmp) cc_final: 0.7629 (mmp) REVERT: A 56 ARG cc_start: 0.8281 (tpm170) cc_final: 0.7994 (tpm170) REVERT: A 63 ARG cc_start: 0.6484 (mmt180) cc_final: 0.6161 (mmt180) REVERT: A 76 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8258 (tt) REVERT: A 299 GLN cc_start: 0.6743 (mt0) cc_final: 0.6527 (mt0) REVERT: A 498 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.6107 (mp) REVERT: A 541 GLU cc_start: 0.8275 (pt0) cc_final: 0.7883 (pm20) outliers start: 32 outliers final: 22 residues processed: 150 average time/residue: 0.2195 time to fit residues: 48.7610 Evaluate side-chains 147 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 184 SER 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 460 SER 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 76 LEU Chi-restraints excluded: chain A residue 139 MET 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 339 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 0.0070 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.5204 ------------------------------------------------------------------------------- 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: 0.7797 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11608 Z= 0.306 Angle : 0.634 9.658 15750 Z= 0.339 Chirality : 0.045 0.196 1814 Planarity : 0.005 0.052 1918 Dihedral : 15.383 151.393 1696 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.81 % Allowed : 13.91 % Favored : 83.28 % 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: 0.16 (0.24), residues: 1388 helix: 1.05 (0.18), residues: 906 sheet: -3.21 (0.73), residues: 30 loop : -1.58 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 613 HIS 0.007 0.001 HIS B 615 PHE 0.038 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 162 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: B 63 ARG cc_start: 0.6600 (mmt180) cc_final: 0.6236 (mpt180) REVERT: B 180 GLN cc_start: 0.6971 (mt0) cc_final: 0.6626 (mt0) REVERT: B 254 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 562 ASP cc_start: 0.8060 (m-30) cc_final: 0.7615 (m-30) REVERT: B 691 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6973 (ptm160) REVERT: A 56 ARG cc_start: 0.8273 (tpm170) cc_final: 0.7813 (tpm170) REVERT: A 62 MET cc_start: 0.7979 (mtp) cc_final: 0.7569 (mtm) REVERT: A 63 ARG cc_start: 0.6432 (mmt180) cc_final: 0.6141 (mmt180) REVERT: A 76 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8172 (tt) REVERT: A 299 GLN cc_start: 0.6792 (mt0) cc_final: 0.6541 (mt0) REVERT: A 541 GLU cc_start: 0.8344 (pt0) cc_final: 0.7880 (pm20) outliers start: 34 outliers final: 27 residues processed: 148 average time/residue: 0.2382 time to fit residues: 53.0953 Evaluate side-chains 151 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 184 SER 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 409 ILE Chi-restraints excluded: chain B residue 460 SER 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 579 ILE Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 339 THR 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: 1.9990 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7783 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11608 Z= 0.265 Angle : 0.616 8.989 15750 Z= 0.331 Chirality : 0.044 0.222 1814 Planarity : 0.005 0.051 1918 Dihedral : 15.038 147.547 1696 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 2.65 % Allowed : 14.49 % Favored : 82.86 % 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: 0.18 (0.24), residues: 1388 helix: 1.07 (0.18), residues: 906 sheet: -3.19 (0.72), residues: 30 loop : -1.57 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.006 0.001 HIS B 615 PHE 0.062 0.002 PHE A 627 TYR 0.016 0.001 TYR A 572 ARG 0.002 0.000 ARG B 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 156 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.232 Fit side-chains REVERT: B 63 ARG cc_start: 0.6599 (mmt180) cc_final: 0.6397 (mpt180) REVERT: B 139 MET cc_start: 0.8219 (ttt) cc_final: 0.7982 (ttt) REVERT: B 180 GLN cc_start: 0.6971 (mt0) cc_final: 0.6633 (mt0) REVERT: B 254 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7070 (mm-30) REVERT: B 475 PHE cc_start: 0.9051 (m-80) cc_final: 0.8761 (m-80) REVERT: B 562 ASP cc_start: 0.8044 (m-30) cc_final: 0.7559 (m-30) REVERT: B 691 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6888 (ptm160) REVERT: A 56 ARG cc_start: 0.8282 (tpm170) cc_final: 0.7814 (tpm170) REVERT: A 62 MET cc_start: 0.7940 (mtp) cc_final: 0.7540 (mtm) REVERT: A 63 ARG cc_start: 0.6412 (mmt180) cc_final: 0.6017 (mmt180) REVERT: A 76 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8175 (tt) REVERT: A 299 GLN cc_start: 0.6828 (mt0) cc_final: 0.6598 (mt0) REVERT: A 541 GLU cc_start: 0.8316 (pt0) cc_final: 0.7874 (pm20) outliers start: 32 outliers final: 23 residues processed: 142 average time/residue: 0.2184 time to fit residues: 45.9214 Evaluate side-chains 145 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 171 TYR Chi-restraints excluded: chain B residue 184 SER 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 409 ILE Chi-restraints excluded: chain B residue 460 SER 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 579 ILE Chi-restraints excluded: chain B residue 677 CYS 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 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 Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 691 ARG 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: 0.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 25 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.0020 chunk 104 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1969 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= 0.182 Angle : 0.575 8.854 15750 Z= 0.306 Chirality : 0.042 0.184 1814 Planarity : 0.005 0.048 1918 Dihedral : 14.423 147.679 1696 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.82 % Allowed : 15.48 % Favored : 82.70 % 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: 1.24 (0.18), residues: 906 sheet: -2.73 (0.74), residues: 34 loop : -1.56 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 613 HIS 0.004 0.001 HIS A 617 PHE 0.030 0.001 PHE B 513 TYR 0.013 0.001 TYR A 572 ARG 0.002 0.000 ARG B 197 *********************** 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 152 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.286 Fit side-chains REVERT: B 63 ARG cc_start: 0.6560 (mmt180) cc_final: 0.6355 (mpt180) REVERT: B 72 ASP cc_start: 0.7949 (t0) cc_final: 0.7729 (t0) REVERT: B 180 GLN cc_start: 0.6950 (mt0) cc_final: 0.6616 (mt0) REVERT: B 254 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7053 (mm-30) REVERT: B 286 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7543 (pp20) REVERT: B 488 ASP cc_start: 0.7981 (t70) cc_final: 0.7643 (t0) REVERT: B 562 ASP cc_start: 0.8087 (m-30) cc_final: 0.7601 (m-30) REVERT: B 691 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6557 (ptm160) REVERT: A 56 ARG cc_start: 0.8265 (tpm170) cc_final: 0.7744 (tpm170) REVERT: A 62 MET cc_start: 0.7930 (mtp) cc_final: 0.7513 (mtm) REVERT: A 63 ARG cc_start: 0.6399 (mmt180) cc_final: 0.5955 (mmt180) REVERT: A 76 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8103 (tt) REVERT: A 286 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7762 (pp20) REVERT: A 299 GLN cc_start: 0.6831 (mt0) cc_final: 0.6621 (mt0) REVERT: A 541 GLU cc_start: 0.8303 (pt0) cc_final: 0.7857 (pm20) outliers start: 22 outliers final: 13 residues processed: 144 average time/residue: 0.2106 time to fit residues: 45.0869 Evaluate side-chains 137 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 409 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 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 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 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: 0.7980 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 0.0470 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 131 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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: 0.7716 moved from start: 0.2065 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= 0.197 Angle : 0.583 8.241 15750 Z= 0.310 Chirality : 0.043 0.227 1814 Planarity : 0.005 0.047 1918 Dihedral : 14.194 148.562 1696 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % 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: 0.38 (0.24), residues: 1388 helix: 1.23 (0.18), residues: 906 sheet: -2.61 (0.74), residues: 34 loop : -1.55 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 PHE 0.039 0.002 PHE B 465 TYR 0.035 0.001 TYR B 246 ARG 0.002 0.000 ARG B 678 *********************** 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 143 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.395 Fit side-chains REVERT: B 63 ARG cc_start: 0.6510 (mmt180) cc_final: 0.6305 (mpt180) REVERT: B 76 LEU cc_start: 0.8523 (tt) cc_final: 0.8273 (tt) REVERT: B 139 MET cc_start: 0.8088 (ttt) cc_final: 0.7753 (ttt) REVERT: B 180 GLN cc_start: 0.6977 (mt0) cc_final: 0.6644 (mt0) REVERT: B 246 TYR cc_start: 0.8420 (m-80) cc_final: 0.8210 (m-80) REVERT: B 254 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7084 (mm-30) REVERT: B 286 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7591 (pp20) REVERT: B 562 ASP cc_start: 0.8109 (m-30) cc_final: 0.7646 (m-30) REVERT: B 691 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6649 (ptm160) REVERT: A 62 MET cc_start: 0.7959 (mtp) cc_final: 0.7533 (mtm) REVERT: A 63 ARG cc_start: 0.6426 (mmt180) cc_final: 0.5990 (mmt180) REVERT: A 76 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8152 (tt) REVERT: A 286 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7787 (pp20) REVERT: A 299 GLN cc_start: 0.6802 (mt0) cc_final: 0.6573 (mt0) REVERT: A 541 GLU cc_start: 0.8325 (pt0) cc_final: 0.7817 (pm20) REVERT: A 627 PHE cc_start: 0.4397 (m-80) cc_final: 0.3970 (m-80) REVERT: A 691 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6985 (ptt-90) outliers start: 21 outliers final: 14 residues processed: 136 average time/residue: 0.2236 time to fit residues: 45.0888 Evaluate side-chains 138 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 409 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 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 171 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 691 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 0.0060 chunk 126 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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: 0.7702 moved from start: 0.2106 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= 0.190 Angle : 0.579 8.636 15750 Z= 0.308 Chirality : 0.043 0.208 1814 Planarity : 0.005 0.047 1918 Dihedral : 14.012 149.985 1696 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.74 % Allowed : 16.23 % Favored : 82.04 % 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: 0.42 (0.24), residues: 1388 helix: 1.27 (0.18), residues: 906 sheet: -2.57 (0.74), residues: 34 loop : -1.54 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.004 0.001 HIS A 615 PHE 0.035 0.002 PHE B 627 TYR 0.032 0.001 TYR B 246 ARG 0.001 0.000 ARG B 450 ********************** 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 143 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.351 Fit side-chains REVERT: B 63 ARG cc_start: 0.6529 (mmt180) cc_final: 0.6326 (mpt180) REVERT: B 76 LEU cc_start: 0.8560 (tt) cc_final: 0.8318 (tt) REVERT: B 139 MET cc_start: 0.8052 (ttt) cc_final: 0.7710 (ttt) REVERT: B 180 GLN cc_start: 0.6973 (mt0) cc_final: 0.6645 (mt0) REVERT: B 246 TYR cc_start: 0.8355 (m-80) cc_final: 0.8133 (m-80) REVERT: B 254 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7100 (mm-30) REVERT: B 286 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7635 (pp20) REVERT: B 562 ASP cc_start: 0.8111 (m-30) cc_final: 0.7636 (m-30) REVERT: B 691 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6617 (ptm160) REVERT: A 62 MET cc_start: 0.7947 (mtp) cc_final: 0.7514 (mtm) REVERT: A 63 ARG cc_start: 0.6436 (mmt180) cc_final: 0.6012 (mmt180) REVERT: A 286 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7935 (pp20) REVERT: A 299 GLN cc_start: 0.6796 (mt0) cc_final: 0.6566 (mt0) REVERT: A 541 GLU cc_start: 0.8315 (pt0) cc_final: 0.7820 (pm20) REVERT: A 680 LEU cc_start: 0.7213 (mm) cc_final: 0.6977 (mt) outliers start: 21 outliers final: 15 residues processed: 135 average time/residue: 0.2277 time to fit residues: 45.3709 Evaluate side-chains 140 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 184 SER 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 461 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 403 VAL 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: 3.9990 chunk 100 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 0.0270 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.166530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132823 restraints weight = 13611.519| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.83 r_work: 0.3401 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2206 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 : 0.581 8.766 15750 Z= 0.309 Chirality : 0.043 0.213 1814 Planarity : 0.005 0.046 1918 Dihedral : 13.816 152.108 1696 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.49 % Allowed : 16.80 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1388 helix: 1.24 (0.18), residues: 920 sheet: -2.51 (0.74), residues: 34 loop : -1.74 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.004 0.001 HIS A 615 PHE 0.059 0.002 PHE B 627 TYR 0.030 0.001 TYR B 246 ARG 0.001 0.000 ARG A 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2395.63 seconds wall clock time: 43 minutes 41.40 seconds (2621.40 seconds total)