Starting phenix.real_space_refine on Sat Aug 3 23:27:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpp_41480/08_2024/8tpp_41480.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpp_41480/08_2024/8tpp_41480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpp_41480/08_2024/8tpp_41480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpp_41480/08_2024/8tpp_41480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpp_41480/08_2024/8tpp_41480.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpp_41480/08_2024/8tpp_41480.cif" } resolution = 3.64 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= 0.000 sd= 0.002 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 Ca 4 9.91 5 S 38 5.16 5 C 5968 2.51 5 N 1524 2.21 5 O 1582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 556": "OD1" <-> "OD2" Residue "B TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9116 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4556 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 23, 'TRANS': 560} Chain breaks: 8 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4556 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 23, 'TRANS': 560} Chain breaks: 8 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.79, per 1000 atoms: 0.64 Number of scatterers: 9116 At special positions: 0 Unit cell: (86.45, 139.23, 100.1, 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) Ca 4 19.99 S 38 16.00 O 1582 8.00 N 1524 7.00 C 5968 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: 3.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 74.1% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.552A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.728A pdb=" N ASP A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 152 through 164 Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.701A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.841A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 217 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.637A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 319 removed outlier: 3.614A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 358 Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 362 through 392 removed outlier: 5.143A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 Processing helix chain 'A' and resid 431 through 451 removed outlier: 3.923A pdb=" N ASN A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 465 removed outlier: 3.658A pdb=" N TYR A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 500 through 518 removed outlier: 3.766A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 545 removed outlier: 3.564A pdb=" N CYS A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.626A pdb=" N ALA A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 585 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 625 Processing helix chain 'A' and resid 630 through 642 Processing helix chain 'A' and resid 701 through 715 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.551A pdb=" N PHE B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.728A pdb=" N ASP B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 152 through 164 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.700A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 removed outlier: 3.841A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 217 through 246 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.637A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 319 removed outlier: 3.614A pdb=" N PHE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 358 Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 362 through 392 removed outlier: 5.144A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 408 Processing helix chain 'B' and resid 431 through 451 removed outlier: 3.922A pdb=" N ASN B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 removed outlier: 3.658A pdb=" N TYR B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 500 through 518 removed outlier: 3.766A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.565A pdb=" N CYS B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.625A pdb=" N ALA B 564 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 585 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 625 Processing helix chain 'B' and resid 630 through 642 Processing helix chain 'B' and resid 701 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267 removed outlier: 4.010A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 267 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 59 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 267 removed outlier: 4.010A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 267 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2860 1.34 - 1.46: 2385 1.46 - 1.58: 4035 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 9342 Sorted by residual: bond pdb=" C ILE B 201 " pdb=" N PRO B 202 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.28e-02 6.10e+03 2.44e+00 bond pdb=" C ILE A 201 " pdb=" N PRO A 202 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.31e+00 bond pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.20e+00 bond pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.17e+00 bond pdb=" CB GLU B 62 " pdb=" CG GLU B 62 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 ... (remaining 9337 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.03: 181 106.03 - 113.03: 5031 113.03 - 120.03: 3285 120.03 - 127.03: 4079 127.03 - 134.02: 130 Bond angle restraints: 12706 Sorted by residual: angle pdb=" N THR A 340 " pdb=" CA THR A 340 " pdb=" C THR A 340 " ideal model delta sigma weight residual 109.81 116.05 -6.24 2.21e+00 2.05e-01 7.98e+00 angle pdb=" N THR B 340 " pdb=" CA THR B 340 " pdb=" C THR B 340 " ideal model delta sigma weight residual 109.81 116.00 -6.19 2.21e+00 2.05e-01 7.85e+00 angle pdb=" CA GLU A 62 " pdb=" CB GLU A 62 " pdb=" CG GLU A 62 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.70e+00 angle pdb=" CA GLU B 62 " pdb=" CB GLU B 62 " pdb=" CG GLU B 62 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.69e+00 angle pdb=" N GLU A 264 " pdb=" CA GLU A 264 " pdb=" C GLU A 264 " ideal model delta sigma weight residual 112.93 109.97 2.96 1.33e+00 5.65e-01 4.94e+00 ... (remaining 12701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4668 17.46 - 34.92: 594 34.92 - 52.38: 139 52.38 - 69.84: 23 69.84 - 87.30: 8 Dihedral angle restraints: 5432 sinusoidal: 2026 harmonic: 3406 Sorted by residual: dihedral pdb=" CG ARG B 490 " pdb=" CD ARG B 490 " pdb=" NE ARG B 490 " pdb=" CZ ARG B 490 " ideal model delta sinusoidal sigma weight residual 90.00 134.09 -44.09 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG A 490 " pdb=" CD ARG A 490 " pdb=" NE ARG A 490 " pdb=" CZ ARG A 490 " ideal model delta sinusoidal sigma weight residual 90.00 134.03 -44.03 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG B 284 " pdb=" CD ARG B 284 " pdb=" NE ARG B 284 " pdb=" CZ ARG B 284 " ideal model delta sinusoidal sigma weight residual 90.00 132.71 -42.71 2 1.50e+01 4.44e-03 9.81e+00 ... (remaining 5429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1159 0.045 - 0.091: 234 0.091 - 0.136: 49 0.136 - 0.181: 2 0.181 - 0.226: 2 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CB VAL B 134 " pdb=" CA VAL B 134 " pdb=" CG1 VAL B 134 " pdb=" CG2 VAL B 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL A 134 " pdb=" CA VAL A 134 " pdb=" CG1 VAL A 134 " pdb=" CG2 VAL A 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1443 not shown) Planarity restraints: 1592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 62 " -0.007 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" CD GLU A 62 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU A 62 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 62 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 62 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" CD GLU B 62 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU B 62 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU B 62 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 201 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 202 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " -0.021 5.00e-02 4.00e+02 ... (remaining 1589 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1617 2.76 - 3.30: 8695 3.30 - 3.83: 15211 3.83 - 4.37: 15299 4.37 - 4.90: 28303 Nonbonded interactions: 69125 Sorted by model distance: nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR B 26 " pdb=" O ALA B 36 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR A 26 " pdb=" O ALA A 36 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR B 555 " pdb=" O SER B 557 " model vdw 2.349 3.040 ... (remaining 69120 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.500 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.060 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.003 0.032 9342 Z= 0.175 Angle : 0.526 6.790 12706 Z= 0.281 Chirality : 0.038 0.226 1446 Planarity : 0.004 0.036 1592 Dihedral : 16.551 87.300 3212 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.11 % Allowed : 23.92 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.18 (0.26), residues: 1132 helix: 2.43 (0.18), residues: 800 sheet: -0.42 (0.82), residues: 44 loop : -1.19 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.002 0.001 HIS A 611 PHE 0.014 0.001 PHE A 379 TYR 0.008 0.001 TYR A 188 ARG 0.006 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.999 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1714 time to fit residues: 19.1060 Evaluate side-chains 68 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.3980 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN B 58 HIS B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9342 Z= 0.217 Angle : 0.525 6.940 12706 Z= 0.271 Chirality : 0.039 0.161 1446 Planarity : 0.004 0.038 1592 Dihedral : 3.617 14.959 1238 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.16 % Allowed : 22.51 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.61 (0.25), residues: 1132 helix: 2.73 (0.18), residues: 806 sheet: -0.11 (0.81), residues: 44 loop : -1.08 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.004 0.001 HIS B 611 PHE 0.014 0.001 PHE A 379 TYR 0.010 0.001 TYR A 188 ARG 0.006 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.979 Fit side-chains REVERT: A 114 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 125 LYS cc_start: 0.7543 (ttmt) cc_final: 0.7185 (tppt) REVERT: B 125 LYS cc_start: 0.7478 (ttmt) cc_final: 0.7184 (tppt) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.1706 time to fit residues: 24.7838 Evaluate side-chains 83 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.0020 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 0.0870 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 633 GLN A 714 GLN B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9342 Z= 0.153 Angle : 0.487 6.235 12706 Z= 0.250 Chirality : 0.037 0.145 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.572 14.466 1238 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.49 % Allowed : 22.62 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.68 (0.25), residues: 1132 helix: 2.77 (0.18), residues: 806 sheet: 0.11 (0.81), residues: 44 loop : -1.04 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.002 0.001 HIS A 611 PHE 0.011 0.001 PHE A 379 TYR 0.010 0.001 TYR A 188 ARG 0.006 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 1.012 Fit side-chains REVERT: A 125 LYS cc_start: 0.7454 (ttmt) cc_final: 0.7131 (tppt) REVERT: B 125 LYS cc_start: 0.7467 (ttmt) cc_final: 0.7134 (tppt) outliers start: 23 outliers final: 12 residues processed: 94 average time/residue: 0.1565 time to fit residues: 23.0715 Evaluate side-chains 87 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9342 Z= 0.309 Angle : 0.567 6.342 12706 Z= 0.295 Chirality : 0.040 0.149 1446 Planarity : 0.004 0.035 1592 Dihedral : 3.788 15.604 1238 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.90 % Allowed : 22.40 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.28 (0.25), residues: 1132 helix: 2.47 (0.18), residues: 810 sheet: 0.34 (0.79), residues: 44 loop : -1.34 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 159 HIS 0.006 0.001 HIS B 611 PHE 0.019 0.001 PHE A 396 TYR 0.011 0.001 TYR B 279 ARG 0.005 0.001 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 75 time to evaluate : 1.057 Fit side-chains REVERT: A 125 LYS cc_start: 0.7548 (ttmt) cc_final: 0.7265 (tppt) REVERT: B 125 LYS cc_start: 0.7531 (ttmt) cc_final: 0.7303 (tppt) outliers start: 36 outliers final: 26 residues processed: 102 average time/residue: 0.1669 time to fit residues: 26.2742 Evaluate side-chains 95 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 69 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 100 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9342 Z= 0.207 Angle : 0.521 6.231 12706 Z= 0.267 Chirality : 0.038 0.145 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.747 15.158 1238 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.03 % Allowed : 23.92 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.29 (0.25), residues: 1132 helix: 2.51 (0.18), residues: 808 sheet: 0.51 (0.84), residues: 44 loop : -1.45 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.003 0.001 HIS B 611 PHE 0.014 0.001 PHE B 396 TYR 0.011 0.001 TYR A 188 ARG 0.007 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 74 time to evaluate : 1.052 Fit side-chains REVERT: A 125 LYS cc_start: 0.7500 (ttmt) cc_final: 0.7219 (tppt) REVERT: B 125 LYS cc_start: 0.7470 (ttmt) cc_final: 0.7201 (tppt) outliers start: 28 outliers final: 19 residues processed: 93 average time/residue: 0.1672 time to fit residues: 24.1202 Evaluate side-chains 89 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9342 Z= 0.163 Angle : 0.497 6.418 12706 Z= 0.253 Chirality : 0.037 0.149 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.658 15.013 1238 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.46 % Allowed : 23.48 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.43 (0.25), residues: 1132 helix: 2.63 (0.18), residues: 808 sheet: 0.58 (0.85), residues: 44 loop : -1.44 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 235 HIS 0.003 0.001 HIS B 611 PHE 0.012 0.001 PHE A 396 TYR 0.010 0.001 TYR A 188 ARG 0.006 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 72 time to evaluate : 0.996 Fit side-chains REVERT: A 125 LYS cc_start: 0.7479 (ttmt) cc_final: 0.7177 (tppt) REVERT: B 125 LYS cc_start: 0.7463 (ttmt) cc_final: 0.7157 (tppt) outliers start: 32 outliers final: 25 residues processed: 95 average time/residue: 0.1535 time to fit residues: 22.9351 Evaluate side-chains 95 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 70 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9342 Z= 0.201 Angle : 0.510 6.480 12706 Z= 0.261 Chirality : 0.038 0.154 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.648 14.937 1238 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.22 % Allowed : 23.16 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.41 (0.25), residues: 1132 helix: 2.61 (0.18), residues: 808 sheet: 0.60 (0.85), residues: 44 loop : -1.44 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.003 0.001 HIS B 611 PHE 0.014 0.001 PHE A 396 TYR 0.009 0.001 TYR A 188 ARG 0.005 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 72 time to evaluate : 1.009 Fit side-chains REVERT: A 125 LYS cc_start: 0.7484 (ttmt) cc_final: 0.7203 (tppt) REVERT: A 263 TRP cc_start: 0.7977 (OUTLIER) cc_final: 0.7304 (p-90) REVERT: A 701 MET cc_start: 0.6221 (mtm) cc_final: 0.5958 (mtt) REVERT: B 125 LYS cc_start: 0.7480 (ttmt) cc_final: 0.7194 (tppt) outliers start: 39 outliers final: 33 residues processed: 102 average time/residue: 0.1578 time to fit residues: 24.8800 Evaluate side-chains 103 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 69 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9342 Z= 0.182 Angle : 0.504 6.477 12706 Z= 0.257 Chirality : 0.038 0.152 1446 Planarity : 0.003 0.034 1592 Dihedral : 3.634 14.816 1238 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.44 % Allowed : 23.38 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.44 (0.25), residues: 1132 helix: 2.63 (0.18), residues: 808 sheet: 0.65 (0.86), residues: 44 loop : -1.43 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 235 HIS 0.003 0.001 HIS A 611 PHE 0.013 0.001 PHE B 396 TYR 0.011 0.001 TYR A 383 ARG 0.008 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 72 time to evaluate : 1.032 Fit side-chains REVERT: A 125 LYS cc_start: 0.7461 (ttmt) cc_final: 0.7167 (tppt) REVERT: A 263 TRP cc_start: 0.7966 (OUTLIER) cc_final: 0.7301 (p-90) REVERT: B 125 LYS cc_start: 0.7455 (ttmt) cc_final: 0.7180 (tppt) REVERT: B 263 TRP cc_start: 0.7938 (OUTLIER) cc_final: 0.7262 (p-90) outliers start: 41 outliers final: 32 residues processed: 104 average time/residue: 0.1514 time to fit residues: 24.8556 Evaluate side-chains 104 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 70 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 263 TRP Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.7980 chunk 62 optimal weight: 0.0070 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9342 Z= 0.151 Angle : 0.495 6.455 12706 Z= 0.250 Chirality : 0.037 0.151 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.600 14.664 1238 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.81 % Allowed : 24.78 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.50 (0.25), residues: 1132 helix: 2.68 (0.18), residues: 810 sheet: 0.61 (0.87), residues: 44 loop : -1.44 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 235 HIS 0.002 0.001 HIS A 611 PHE 0.012 0.001 PHE B 379 TYR 0.010 0.001 TYR A 188 ARG 0.008 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 1.015 Fit side-chains REVERT: A 125 LYS cc_start: 0.7424 (ttmt) cc_final: 0.7141 (tppt) REVERT: A 263 TRP cc_start: 0.7957 (OUTLIER) cc_final: 0.7237 (p-90) REVERT: B 125 LYS cc_start: 0.7423 (ttmt) cc_final: 0.7122 (tppt) outliers start: 26 outliers final: 23 residues processed: 90 average time/residue: 0.2025 time to fit residues: 27.9026 Evaluate side-chains 94 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9342 Z= 0.182 Angle : 0.509 6.499 12706 Z= 0.257 Chirality : 0.038 0.152 1446 Planarity : 0.003 0.034 1592 Dihedral : 3.596 14.675 1238 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.14 % Allowed : 24.35 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.42 (0.25), residues: 1132 helix: 2.64 (0.18), residues: 812 sheet: 0.59 (0.87), residues: 44 loop : -1.56 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 235 HIS 0.003 0.001 HIS B 611 PHE 0.013 0.001 PHE B 379 TYR 0.009 0.001 TYR A 383 ARG 0.008 0.000 ARG A 710 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 1.005 Fit side-chains REVERT: A 62 GLU cc_start: 0.7062 (mp0) cc_final: 0.6664 (mp0) REVERT: A 125 LYS cc_start: 0.7433 (ttmt) cc_final: 0.7146 (tppt) REVERT: A 263 TRP cc_start: 0.7989 (OUTLIER) cc_final: 0.7261 (p-90) REVERT: B 125 LYS cc_start: 0.7430 (ttmt) cc_final: 0.7125 (tppt) REVERT: B 263 TRP cc_start: 0.7951 (OUTLIER) cc_final: 0.7208 (p-90) outliers start: 29 outliers final: 27 residues processed: 95 average time/residue: 0.1534 time to fit residues: 23.1962 Evaluate side-chains 99 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 70 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 263 TRP Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 66 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104554 restraints weight = 13875.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106605 restraints weight = 9261.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107910 restraints weight = 7227.036| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9342 Z= 0.155 Angle : 0.504 6.473 12706 Z= 0.254 Chirality : 0.037 0.151 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.584 14.576 1238 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.35 % Allowed : 24.24 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.49 (0.25), residues: 1132 helix: 2.68 (0.18), residues: 812 sheet: 0.55 (0.87), residues: 44 loop : -1.48 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 235 HIS 0.002 0.001 HIS A 611 PHE 0.012 0.001 PHE B 379 TYR 0.009 0.001 TYR A 188 ARG 0.008 0.000 ARG A 710 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1661.87 seconds wall clock time: 30 minutes 55.70 seconds (1855.70 seconds total)