Starting phenix.real_space_refine on Fri Jul 19 01:59:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/07_2024/8x61_38077.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/07_2024/8x61_38077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/07_2024/8x61_38077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/07_2024/8x61_38077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/07_2024/8x61_38077.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/07_2024/8x61_38077.cif" } resolution = 3.05 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= 0.023 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 6 5.49 5 S 32 5.16 5 C 3679 2.51 5 N 1009 2.21 5 O 1011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5737 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1680 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1662 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 208} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1141 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain breaks: 2 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1192 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.28, per 1000 atoms: 0.75 Number of scatterers: 5737 At special positions: 0 Unit cell: (72.24, 75.6, 107.52, 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 32 16.00 P 6 15.00 O 1011 8.00 N 1009 7.00 C 3679 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 64.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.198A pdb=" N GLN A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 108 Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.696A pdb=" N VAL A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 169 through 185 Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.701A pdb=" N ILE A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 73 through 79 Processing helix chain 'B' and resid 95 through 108 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.538A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 169 through 185 Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.931A pdb=" N ARG B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 351 removed outlier: 4.328A pdb=" N TYR C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS C 351 " --> pdb=" O ASP C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 380 removed outlier: 3.769A pdb=" N ILE C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 368 " --> pdb=" O ILE C 364 " (cutoff:3.500A) Proline residue: C 369 - end of helix Processing helix chain 'C' and resid 506 through 532 removed outlier: 3.522A pdb=" N LEU C 512 " --> pdb=" O MET C 508 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE C 518 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 532 " --> pdb=" O SER C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 543 removed outlier: 3.814A pdb=" N ILE C 536 " --> pdb=" O ARG C 532 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C 543 " --> pdb=" O GLN C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 579 Proline residue: C 552 - end of helix Processing helix chain 'C' and resid 600 through 628 Processing helix chain 'D' and resid 335 through 351 removed outlier: 3.864A pdb=" N TYR D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 351 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 379 removed outlier: 3.848A pdb=" N LEU D 368 " --> pdb=" O ILE D 364 " (cutoff:3.500A) Proline residue: D 369 - end of helix Processing helix chain 'D' and resid 502 through 532 removed outlier: 4.554A pdb=" N MET D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE D 509 " --> pdb=" O VAL D 505 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU D 512 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET D 513 " --> pdb=" O ILE D 509 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 517 " --> pdb=" O MET D 513 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 543 removed outlier: 3.574A pdb=" N ILE D 536 " --> pdb=" O ARG D 532 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN D 537 " --> pdb=" O ARG D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 579 Proline residue: D 552 - end of helix Processing helix chain 'D' and resid 600 through 628 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 25 removed outlier: 5.572A pdb=" N GLN A 19 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS A 9 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE A 23 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU A 5 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N MET A 25 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG A 3 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 7 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA A 56 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.887A pdb=" N ARG A 206 " --> pdb=" O MET A 30 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR A 209 " --> pdb=" O HIS A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 25 removed outlier: 6.559A pdb=" N ALA B 17 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA B 10 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN B 19 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER B 8 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL B 21 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 6 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 7 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 56 " --> pdb=" O VAL B 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 84 removed outlier: 3.832A pdb=" N ARG B 206 " --> pdb=" O MET B 30 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR B 209 " --> pdb=" O HIS B 216 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1122 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: 1.47 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 995 1.32 - 1.45: 1408 1.45 - 1.57: 3370 1.57 - 1.69: 10 1.69 - 1.81: 56 Bond restraints: 5839 Sorted by residual: bond pdb=" C PRO D 369 " pdb=" O PRO D 369 " ideal model delta sigma weight residual 1.238 1.202 0.036 1.33e-02 5.65e+03 7.28e+00 bond pdb=" N LEU D 368 " pdb=" CA LEU D 368 " ideal model delta sigma weight residual 1.463 1.481 -0.018 6.90e-03 2.10e+04 6.52e+00 bond pdb=" O5' ATP B 301 " pdb=" PA ATP B 301 " ideal model delta sigma weight residual 1.579 1.602 -0.023 1.10e-02 8.26e+03 4.47e+00 bond pdb=" O5' ATP A 301 " pdb=" PA ATP A 301 " ideal model delta sigma weight residual 1.579 1.600 -0.021 1.10e-02 8.26e+03 3.77e+00 bond pdb=" O2B ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 1.529 1.488 0.041 2.20e-02 2.07e+03 3.49e+00 ... (remaining 5834 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.18: 146 106.18 - 113.17: 3297 113.17 - 120.15: 1976 120.15 - 127.13: 2433 127.13 - 134.11: 68 Bond angle restraints: 7920 Sorted by residual: angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 133.08 6.79 1.00e+00 1.00e+00 4.61e+01 angle pdb=" PB ATP A 301 " pdb=" O3B ATP A 301 " pdb=" PG ATP A 301 " ideal model delta sigma weight residual 139.87 133.91 5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" CA PRO D 552 " pdb=" N PRO D 552 " pdb=" CD PRO D 552 " ideal model delta sigma weight residual 112.00 106.28 5.72 1.40e+00 5.10e-01 1.67e+01 angle pdb=" N THR B 165 " pdb=" CA THR B 165 " pdb=" C THR B 165 " ideal model delta sigma weight residual 114.75 110.18 4.57 1.26e+00 6.30e-01 1.31e+01 angle pdb=" C ASP B 87 " pdb=" N HIS B 88 " pdb=" CA HIS B 88 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.52e+00 ... (remaining 7915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3105 17.96 - 35.91: 263 35.91 - 53.87: 100 53.87 - 71.82: 12 71.82 - 89.78: 9 Dihedral angle restraints: 3489 sinusoidal: 1349 harmonic: 2140 Sorted by residual: dihedral pdb=" CB GLU A 29 " pdb=" CG GLU A 29 " pdb=" CD GLU A 29 " pdb=" OE1 GLU A 29 " ideal model delta sinusoidal sigma weight residual 0.00 89.78 -89.78 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA HIS A 195 " pdb=" C HIS A 195 " pdb=" N ASP A 196 " pdb=" CA ASP A 196 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CB MET C 360 " pdb=" CG MET C 360 " pdb=" SD MET C 360 " pdb=" CE MET C 360 " ideal model delta sinusoidal sigma weight residual -180.00 -123.41 -56.59 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 717 0.040 - 0.079: 179 0.079 - 0.119: 38 0.119 - 0.158: 10 0.158 - 0.198: 3 Chirality restraints: 947 Sorted by residual: chirality pdb=" C2' ATP B 301 " pdb=" C1' ATP B 301 " pdb=" C3' ATP B 301 " pdb=" O2' ATP B 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.48 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C2' ATP A 301 " pdb=" C1' ATP A 301 " pdb=" C3' ATP A 301 " pdb=" O2' ATP A 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.50 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA ILE B 102 " pdb=" N ILE B 102 " pdb=" C ILE B 102 " pdb=" CB ILE B 102 " both_signs ideal model delta sigma weight residual False 2.43 2.27 0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 944 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 551 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO D 552 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO D 552 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 552 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 367 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C THR D 367 " 0.028 2.00e-02 2.50e+03 pdb=" O THR D 367 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU D 368 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 631 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO C 632 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 632 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 632 " -0.019 5.00e-02 4.00e+02 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 794 2.75 - 3.29: 5393 3.29 - 3.83: 9137 3.83 - 4.36: 10919 4.36 - 4.90: 19068 Nonbonded interactions: 45311 Sorted by model distance: nonbonded pdb=" O ASP A 169 " pdb=" OG SER A 173 " model vdw 2.218 2.440 nonbonded pdb=" NE2 GLN A 86 " pdb=" OD1 ASN B 167 " model vdw 2.230 2.520 nonbonded pdb=" ND2 ASN A 184 " pdb=" O VAL A 188 " model vdw 2.232 2.520 nonbonded pdb=" OE2 GLU A 181 " pdb=" OH TYR A 205 " model vdw 2.242 2.440 nonbonded pdb=" O ASN A 198 " pdb=" NH1 ARG A 202 " model vdw 2.295 2.520 ... (remaining 45306 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' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 through 71 or (resid 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 through 196 or (resid 197 thro \ ugh 198 and (name N or name CA or name C or name O or name CB )) or resid 199 th \ rough 216 or resid 301)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 334 through 379 or resid 502 through 630 or (resid 631 and \ (name N or name CA or name C or name O or name CB )) or resid 632)) selection = (chain 'D' and (resid 334 through 341 or (resid 342 and (name N or name CA or na \ me C or name O or name CB )) or resid 343 through 345 or (resid 346 through 347 \ and (name N or name CA or name C or name O or name CB )) or resid 348 through 35 \ 2 or (resid 353 through 354 and (name N or name CA or name C or name O or name C \ B )) or resid 355 through 379 or (resid 502 through 505 and (name N or name CA o \ r name C or name O or name CB )) or resid 506 through 533 or (resid 534 and (nam \ e N or name CA or name C or name O or name CB )) or resid 535 through 576 or (re \ sid 577 through 578 and (name N or name CA or name C or name O or name CB )) or \ resid 579 or (resid 597 and (name N or name CA or name C or name O or name CB )) \ or resid 598 or (resid 599 through 600 and (name N or name CA or name C or name \ O or name CB )) or resid 601 through 602 or (resid 603 and (name N or name CA o \ r name C or name O or name CB )) or resid 604 or (resid 605 and (name N or name \ CA or name C or name O or name CB )) or resid 606 through 632)) } 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.140 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.004 0.043 5839 Z= 0.258 Angle : 0.604 7.946 7920 Z= 0.333 Chirality : 0.039 0.198 947 Planarity : 0.005 0.110 984 Dihedral : 15.998 89.776 2109 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.34 % Allowed : 12.16 % Favored : 87.50 % 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: 0.61 (0.30), residues: 740 helix: 1.42 (0.24), residues: 447 sheet: -0.44 (0.62), residues: 50 loop : -1.33 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 616 HIS 0.008 0.001 HIS A 195 PHE 0.010 0.001 PHE D 518 TYR 0.006 0.001 TYR A 205 ARG 0.003 0.000 ARG C 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.630 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.1929 time to fit residues: 19.4634 Evaluate side-chains 78 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 539 GLN Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5839 Z= 0.259 Angle : 0.585 7.338 7920 Z= 0.297 Chirality : 0.039 0.164 947 Planarity : 0.004 0.062 984 Dihedral : 10.851 89.316 875 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.88 % Allowed : 13.53 % Favored : 84.59 % 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: 1.44 (0.30), residues: 740 helix: 2.30 (0.24), residues: 446 sheet: -0.03 (0.64), residues: 62 loop : -1.53 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 616 HIS 0.011 0.001 HIS A 195 PHE 0.019 0.002 PHE D 518 TYR 0.008 0.001 TYR D 339 ARG 0.005 0.000 ARG C 533 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.581 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.1942 time to fit residues: 22.0473 Evaluate side-chains 86 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5839 Z= 0.235 Angle : 0.544 7.295 7920 Z= 0.277 Chirality : 0.038 0.160 947 Planarity : 0.004 0.051 984 Dihedral : 10.887 88.496 872 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.77 % Allowed : 13.36 % Favored : 82.88 % 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: 1.71 (0.31), residues: 740 helix: 2.59 (0.24), residues: 446 sheet: 0.14 (0.66), residues: 62 loop : -1.64 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 616 HIS 0.008 0.001 HIS A 195 PHE 0.020 0.002 PHE D 518 TYR 0.006 0.001 TYR A 205 ARG 0.003 0.000 ARG C 533 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.618 Fit side-chains REVERT: C 374 MET cc_start: 0.6938 (mtt) cc_final: 0.6613 (mtt) REVERT: D 626 HIS cc_start: 0.5965 (OUTLIER) cc_final: 0.5569 (t-90) outliers start: 22 outliers final: 14 residues processed: 103 average time/residue: 0.1920 time to fit residues: 25.5144 Evaluate side-chains 97 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 626 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.0040 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5839 Z= 0.185 Angle : 0.520 7.193 7920 Z= 0.265 Chirality : 0.037 0.155 947 Planarity : 0.003 0.043 984 Dihedral : 10.338 87.062 872 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.94 % Allowed : 14.38 % Favored : 81.68 % 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: 1.95 (0.31), residues: 740 helix: 2.83 (0.24), residues: 446 sheet: 0.23 (0.68), residues: 62 loop : -1.67 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 616 HIS 0.005 0.001 HIS D 342 PHE 0.020 0.001 PHE D 518 TYR 0.005 0.001 TYR C 339 ARG 0.003 0.000 ARG C 533 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.596 Fit side-chains REVERT: B 15 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.5326 (ttp-170) REVERT: B 83 MET cc_start: 0.8317 (tpt) cc_final: 0.7939 (tpp) REVERT: C 374 MET cc_start: 0.6903 (mtt) cc_final: 0.6607 (mtt) REVERT: C 526 ARG cc_start: 0.7255 (tpt170) cc_final: 0.7006 (mmt180) outliers start: 23 outliers final: 14 residues processed: 97 average time/residue: 0.1850 time to fit residues: 23.2205 Evaluate side-chains 91 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain D residue 514 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5839 Z= 0.267 Angle : 0.566 7.298 7920 Z= 0.287 Chirality : 0.039 0.171 947 Planarity : 0.004 0.039 984 Dihedral : 10.494 77.469 870 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.45 % Allowed : 14.90 % Favored : 80.65 % 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: 1.82 (0.31), residues: 740 helix: 2.67 (0.24), residues: 448 sheet: 0.51 (0.72), residues: 50 loop : -1.62 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 616 HIS 0.003 0.001 HIS B 195 PHE 0.019 0.002 PHE D 518 TYR 0.007 0.001 TYR C 339 ARG 0.002 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 0.674 Fit side-chains REVERT: B 15 ARG cc_start: 0.6011 (OUTLIER) cc_final: 0.5661 (ttp-170) REVERT: B 207 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7004 (tmm) REVERT: C 374 MET cc_start: 0.6977 (mtt) cc_final: 0.6730 (mtt) REVERT: C 526 ARG cc_start: 0.7271 (tpt170) cc_final: 0.7008 (mmt180) outliers start: 26 outliers final: 19 residues processed: 97 average time/residue: 0.1957 time to fit residues: 24.2999 Evaluate side-chains 99 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 514 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5839 Z= 0.250 Angle : 0.556 7.243 7920 Z= 0.284 Chirality : 0.039 0.165 947 Planarity : 0.003 0.036 984 Dihedral : 10.222 75.368 870 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.45 % Allowed : 15.58 % Favored : 79.97 % 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: 1.76 (0.31), residues: 740 helix: 2.69 (0.24), residues: 448 sheet: 0.30 (0.69), residues: 62 loop : -1.85 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 616 HIS 0.005 0.001 HIS D 342 PHE 0.019 0.001 PHE D 518 TYR 0.005 0.001 TYR D 339 ARG 0.002 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 0.669 Fit side-chains REVERT: A 195 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6500 (p90) REVERT: B 15 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5725 (ttp-170) REVERT: B 83 MET cc_start: 0.8356 (tpt) cc_final: 0.8061 (tpp) REVERT: B 207 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7036 (tmm) REVERT: C 374 MET cc_start: 0.6946 (mtt) cc_final: 0.6732 (mtt) REVERT: C 526 ARG cc_start: 0.7195 (tpt170) cc_final: 0.6912 (mmt180) outliers start: 26 outliers final: 18 residues processed: 100 average time/residue: 0.1952 time to fit residues: 25.1646 Evaluate side-chains 102 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain D residue 514 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5839 Z= 0.240 Angle : 0.555 7.223 7920 Z= 0.282 Chirality : 0.039 0.172 947 Planarity : 0.003 0.034 984 Dihedral : 10.193 75.034 870 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.11 % Allowed : 16.78 % Favored : 79.11 % 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: 1.78 (0.31), residues: 740 helix: 2.71 (0.24), residues: 448 sheet: 0.33 (0.69), residues: 62 loop : -1.85 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 616 HIS 0.003 0.001 HIS D 629 PHE 0.017 0.001 PHE D 518 TYR 0.005 0.001 TYR D 339 ARG 0.002 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.680 Fit side-chains REVERT: A 195 HIS cc_start: 0.7120 (OUTLIER) cc_final: 0.6420 (p-80) REVERT: B 15 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5658 (ttp-170) REVERT: B 83 MET cc_start: 0.8380 (tpt) cc_final: 0.8077 (tpp) REVERT: B 207 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7030 (tmm) REVERT: C 526 ARG cc_start: 0.7201 (tpt170) cc_final: 0.6910 (mmt180) outliers start: 24 outliers final: 18 residues processed: 97 average time/residue: 0.2056 time to fit residues: 25.4835 Evaluate side-chains 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 514 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN D 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5839 Z= 0.212 Angle : 0.549 7.771 7920 Z= 0.280 Chirality : 0.038 0.182 947 Planarity : 0.003 0.033 984 Dihedral : 9.988 73.464 870 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.28 % Allowed : 16.95 % Favored : 78.77 % 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: 1.83 (0.31), residues: 740 helix: 2.75 (0.24), residues: 448 sheet: 0.40 (0.69), residues: 62 loop : -1.85 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 616 HIS 0.005 0.001 HIS D 342 PHE 0.017 0.001 PHE D 518 TYR 0.004 0.001 TYR D 339 ARG 0.002 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 0.651 Fit side-chains REVERT: A 195 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6309 (p-80) REVERT: B 15 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5560 (ttp-170) REVERT: B 207 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7012 (tmm) outliers start: 25 outliers final: 20 residues processed: 96 average time/residue: 0.2020 time to fit residues: 24.6986 Evaluate side-chains 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain D residue 508 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5839 Z= 0.293 Angle : 0.598 7.596 7920 Z= 0.304 Chirality : 0.040 0.190 947 Planarity : 0.004 0.032 984 Dihedral : 10.430 77.078 870 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.94 % Allowed : 17.81 % Favored : 78.25 % 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: 1.63 (0.31), residues: 740 helix: 2.52 (0.24), residues: 448 sheet: 0.65 (0.75), residues: 50 loop : -1.76 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 616 HIS 0.003 0.001 HIS B 195 PHE 0.017 0.002 PHE D 518 TYR 0.006 0.001 TYR D 339 ARG 0.003 0.000 ARG D 532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.645 Fit side-chains REVERT: A 195 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6481 (p-80) REVERT: B 207 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7072 (tmm) outliers start: 23 outliers final: 19 residues processed: 97 average time/residue: 0.2077 time to fit residues: 25.4102 Evaluate side-chains 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain D residue 508 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5839 Z= 0.353 Angle : 0.645 7.526 7920 Z= 0.327 Chirality : 0.041 0.196 947 Planarity : 0.004 0.033 984 Dihedral : 10.838 81.358 870 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.94 % Allowed : 17.81 % Favored : 78.25 % 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: 1.39 (0.31), residues: 740 helix: 2.35 (0.24), residues: 448 sheet: 0.52 (0.74), residues: 50 loop : -1.89 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 616 HIS 0.005 0.001 HIS D 342 PHE 0.019 0.002 PHE D 518 TYR 0.006 0.002 TYR D 339 ARG 0.003 0.001 ARG D 532 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 0.640 Fit side-chains REVERT: A 195 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.6519 (p-80) REVERT: B 207 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7116 (tmm) outliers start: 23 outliers final: 19 residues processed: 93 average time/residue: 0.1943 time to fit residues: 23.0220 Evaluate side-chains 100 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain D residue 508 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 chunk 10 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.186045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.161828 restraints weight = 5672.290| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.06 r_work: 0.3678 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5839 Z= 0.218 Angle : 0.564 7.394 7920 Z= 0.287 Chirality : 0.039 0.191 947 Planarity : 0.003 0.032 984 Dihedral : 10.148 73.886 870 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.60 % Allowed : 18.15 % Favored : 78.25 % 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: 1.66 (0.31), residues: 740 helix: 2.63 (0.24), residues: 448 sheet: 0.40 (0.70), residues: 62 loop : -1.98 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 616 HIS 0.003 0.001 HIS D 629 PHE 0.018 0.001 PHE D 518 TYR 0.005 0.001 TYR D 339 ARG 0.002 0.000 ARG D 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.39 seconds wall clock time: 27 minutes 13.85 seconds (1633.85 seconds total)