Starting phenix.real_space_refine on Tue Jan 14 05:15:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x61_38077/01_2025/8x61_38077.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x61_38077/01_2025/8x61_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/cci-nas-00/data/ceres_data/8x61_38077/01_2025/8x61_38077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x61_38077/01_2025/8x61_38077.map" model { file = "/net/cci-nas-00/data/ceres_data/8x61_38077/01_2025/8x61_38077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x61_38077/01_2025/8x61_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. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 4.45, per 1000 atoms: 0.78 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 - 3.00 Amino acid : True - 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: 1.42 Conformation dependent library (CDL) restraints added in 919.9 milliseconds 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: 0.57 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: 1.57 Time building geometry restraints manager: 1.66 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: 0.00 - 1.59: 7737 1.59 - 3.18: 135 3.18 - 4.77: 33 4.77 - 6.36: 11 6.36 - 7.95: 4 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 3.040 nonbonded pdb=" NE2 GLN A 86 " pdb=" OD1 ASN B 167 " model vdw 2.230 3.120 nonbonded pdb=" ND2 ASN A 184 " pdb=" O VAL A 188 " model vdw 2.232 3.120 nonbonded pdb=" OE2 GLU A 181 " pdb=" OH TYR A 205 " model vdw 2.242 3.040 nonbonded pdb=" O ASN A 198 " pdb=" NH1 ARG A 202 " model vdw 2.295 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 2.280 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.600 Find NCS groups from input model: 0.170 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.571 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.2082 time to fit residues: 21.1525 Evaluate side-chains 78 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 0.5980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.0070 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 539 GLN D 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.201163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.171101 restraints weight = 5535.888| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.65 r_work: 0.3548 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1122 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= 0.199 Angle : 0.552 7.180 7920 Z= 0.283 Chirality : 0.038 0.157 947 Planarity : 0.004 0.065 984 Dihedral : 10.413 84.531 875 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.54 % Allowed : 12.33 % Favored : 86.13 % 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: 2.44 (0.24), residues: 446 sheet: 0.04 (0.65), residues: 62 loop : -1.45 (0.37), 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 0.017 0.002 PHE D 518 TYR 0.006 0.001 TYR C 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 to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.634 Fit side-chains REVERT: D 360 MET cc_start: 0.7748 (ttt) cc_final: 0.7477 (tpt) REVERT: D 626 HIS cc_start: 0.5813 (OUTLIER) cc_final: 0.5400 (t-90) outliers start: 9 outliers final: 7 residues processed: 90 average time/residue: 0.1801 time to fit residues: 21.4905 Evaluate side-chains 85 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 182 GLU 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 Chi-restraints excluded: chain D residue 626 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 195 HIS C 539 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.185846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.160122 restraints weight = 5728.686| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.11 r_work: 0.3650 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5839 Z= 0.332 Angle : 0.619 7.454 7920 Z= 0.312 Chirality : 0.040 0.172 947 Planarity : 0.004 0.056 984 Dihedral : 11.466 88.723 872 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.74 % Allowed : 14.04 % Favored : 83.22 % 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: 1.55 (0.31), residues: 740 helix: 2.43 (0.24), residues: 446 sheet: 0.26 (0.71), residues: 50 loop : -1.58 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 616 HIS 0.009 0.001 HIS A 195 PHE 0.019 0.002 PHE D 518 TYR 0.008 0.002 TYR C 339 ARG 0.003 0.000 ARG A 202 *********************** 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 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.559 Fit side-chains REVERT: D 360 MET cc_start: 0.7980 (ttt) cc_final: 0.7750 (tpt) REVERT: D 367 THR cc_start: 0.8378 (t) cc_final: 0.8172 (p) REVERT: D 512 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7135 (mp) outliers start: 16 outliers final: 13 residues processed: 98 average time/residue: 0.1926 time to fit residues: 24.4159 Evaluate side-chains 94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 170 ASP 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 34 THR 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 B residue 212 ASP Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.187194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156429 restraints weight = 5759.486| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.35 r_work: 0.3588 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1790 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= 0.201 Angle : 0.548 8.415 7920 Z= 0.277 Chirality : 0.038 0.159 947 Planarity : 0.003 0.046 984 Dihedral : 10.683 88.508 872 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.25 % Allowed : 13.53 % Favored : 83.22 % 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: 1.80 (0.31), residues: 740 helix: 2.70 (0.24), residues: 446 sheet: 0.18 (0.68), residues: 62 loop : -1.69 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 616 HIS 0.004 0.001 HIS D 342 PHE 0.020 0.001 PHE D 518 TYR 0.006 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 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.621 Fit side-chains REVERT: B 15 ARG cc_start: 0.5685 (OUTLIER) cc_final: 0.5055 (ttp-170) REVERT: B 83 MET cc_start: 0.8446 (tpt) cc_final: 0.7884 (tpp) REVERT: B 212 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6876 (t0) REVERT: C 526 ARG cc_start: 0.7087 (tpt170) cc_final: 0.6772 (mmt180) REVERT: D 574 ILE cc_start: 0.7949 (mm) cc_final: 0.7707 (mt) REVERT: D 626 HIS cc_start: 0.5689 (OUTLIER) cc_final: 0.5307 (t-90) outliers start: 19 outliers final: 12 residues processed: 99 average time/residue: 0.1885 time to fit residues: 24.2152 Evaluate side-chains 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 170 ASP 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 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 626 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.188150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.162727 restraints weight = 5672.081| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.11 r_work: 0.3653 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5839 Z= 0.221 Angle : 0.542 7.229 7920 Z= 0.275 Chirality : 0.038 0.161 947 Planarity : 0.003 0.041 984 Dihedral : 10.621 87.981 870 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.91 % Allowed : 14.90 % Favored : 82.19 % 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: 1.90 (0.31), residues: 740 helix: 2.80 (0.24), residues: 446 sheet: 0.24 (0.69), residues: 62 loop : -1.72 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 616 HIS 0.004 0.001 HIS D 342 PHE 0.020 0.001 PHE D 518 TYR 0.006 0.001 TYR C 339 ARG 0.003 0.000 ARG C 533 *********************** 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 101 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.642 Fit side-chains REVERT: B 15 ARG cc_start: 0.5936 (OUTLIER) cc_final: 0.5252 (ttp-170) REVERT: B 212 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6945 (t0) REVERT: C 526 ARG cc_start: 0.7408 (tpt170) cc_final: 0.7088 (mmt180) REVERT: D 574 ILE cc_start: 0.7911 (mm) cc_final: 0.7683 (mt) outliers start: 17 outliers final: 12 residues processed: 97 average time/residue: 0.2011 time to fit residues: 25.2171 Evaluate side-chains 94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 170 ASP 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 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 B residue 212 ASP Chi-restraints excluded: chain C residue 576 VAL 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 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 50 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.189413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.164031 restraints weight = 5685.594| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.12 r_work: 0.3663 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5839 Z= 0.180 Angle : 0.520 7.139 7920 Z= 0.265 Chirality : 0.037 0.157 947 Planarity : 0.003 0.036 984 Dihedral : 10.336 88.943 870 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.74 % Allowed : 15.07 % Favored : 82.19 % 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: 2.06 (0.31), residues: 740 helix: 2.91 (0.24), residues: 448 sheet: 0.36 (0.70), residues: 62 loop : -1.67 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 616 HIS 0.006 0.001 HIS D 342 PHE 0.019 0.001 PHE D 518 TYR 0.004 0.001 TYR C 339 ARG 0.003 0.000 ARG C 533 *********************** 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 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.625 Fit side-chains REVERT: B 15 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.5030 (ttp-170) REVERT: B 207 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7608 (tmm) REVERT: B 212 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6921 (t0) REVERT: C 526 ARG cc_start: 0.7326 (tpt170) cc_final: 0.6993 (mmt180) REVERT: D 574 ILE cc_start: 0.7839 (mm) cc_final: 0.7618 (mt) outliers start: 16 outliers final: 9 residues processed: 95 average time/residue: 0.1825 time to fit residues: 22.6986 Evaluate side-chains 92 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 170 ASP Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ASP 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 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 chunk 67 optimal weight: 0.0870 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.190535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.165886 restraints weight = 5717.397| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.11 r_work: 0.3720 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5839 Z= 0.169 Angle : 0.510 7.181 7920 Z= 0.257 Chirality : 0.037 0.155 947 Planarity : 0.003 0.034 984 Dihedral : 10.103 89.909 870 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.08 % Allowed : 15.58 % Favored : 81.34 % 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: 2.20 (0.32), residues: 740 helix: 2.95 (0.24), residues: 452 sheet: 0.43 (0.70), residues: 62 loop : -1.54 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 616 HIS 0.003 0.001 HIS D 629 PHE 0.017 0.001 PHE D 518 TYR 0.004 0.001 TYR D 339 ARG 0.002 0.000 ARG C 533 *********************** 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 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.639 Fit side-chains REVERT: B 15 ARG cc_start: 0.5851 (OUTLIER) cc_final: 0.4938 (ttp-170) REVERT: B 76 PHE cc_start: 0.8270 (m-10) cc_final: 0.8026 (m-10) REVERT: B 207 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7517 (tmm) REVERT: B 212 ASP cc_start: 0.7195 (m-30) cc_final: 0.6953 (t0) REVERT: C 526 ARG cc_start: 0.7340 (tpt170) cc_final: 0.7079 (mmt180) REVERT: D 574 ILE cc_start: 0.7862 (mm) cc_final: 0.7614 (mt) outliers start: 18 outliers final: 8 residues processed: 99 average time/residue: 0.1865 time to fit residues: 24.4581 Evaluate side-chains 93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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 159 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 0.0370 chunk 21 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS D 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.189071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.165291 restraints weight = 5654.606| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.05 r_work: 0.3706 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5839 Z= 0.199 Angle : 0.534 7.201 7920 Z= 0.268 Chirality : 0.038 0.158 947 Planarity : 0.003 0.033 984 Dihedral : 10.250 89.034 870 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.74 % Allowed : 15.92 % Favored : 81.34 % 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: 2.13 (0.31), residues: 740 helix: 2.95 (0.24), residues: 448 sheet: 0.43 (0.70), residues: 62 loop : -1.63 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 616 HIS 0.005 0.001 HIS D 342 PHE 0.016 0.001 PHE D 518 TYR 0.006 0.001 TYR A 205 ARG 0.002 0.000 ARG B 206 *********************** 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 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.640 Fit side-chains REVERT: A 182 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6850 (pt0) REVERT: B 15 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.4963 (ttp-170) REVERT: B 207 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7459 (tmm) REVERT: B 212 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6936 (t0) REVERT: C 526 ARG cc_start: 0.7347 (tpt170) cc_final: 0.7089 (mmt180) REVERT: D 574 ILE cc_start: 0.7866 (mm) cc_final: 0.7637 (mt) outliers start: 16 outliers final: 10 residues processed: 93 average time/residue: 0.1931 time to fit residues: 23.5652 Evaluate side-chains 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 83 MET Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ASP 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 61 optimal weight: 0.0670 chunk 47 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 36 optimal weight: 0.0270 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.190673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.166264 restraints weight = 5687.728| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.17 r_work: 0.3709 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5839 Z= 0.164 Angle : 0.526 7.806 7920 Z= 0.267 Chirality : 0.037 0.154 947 Planarity : 0.003 0.032 984 Dihedral : 10.065 89.916 870 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.23 % Allowed : 16.44 % Favored : 81.34 % 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: 2.21 (0.31), residues: 740 helix: 2.95 (0.24), residues: 452 sheet: 0.44 (0.70), residues: 62 loop : -1.51 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 616 HIS 0.003 0.001 HIS A 195 PHE 0.016 0.001 PHE D 518 TYR 0.005 0.001 TYR A 205 ARG 0.002 0.000 ARG C 533 *********************** 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 94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.598 Fit side-chains REVERT: A 182 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6886 (pt0) REVERT: B 15 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.4982 (ttp-170) REVERT: B 76 PHE cc_start: 0.8257 (m-10) cc_final: 0.8020 (m-10) REVERT: B 207 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7559 (tmm) REVERT: B 212 ASP cc_start: 0.7204 (m-30) cc_final: 0.6944 (t0) REVERT: D 574 ILE cc_start: 0.7840 (mm) cc_final: 0.7598 (mt) outliers start: 13 outliers final: 9 residues processed: 89 average time/residue: 0.1888 time to fit residues: 21.9051 Evaluate side-chains 92 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 83 MET Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS D 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164964 restraints weight = 5716.879| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.09 r_work: 0.3710 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5839 Z= 0.198 Angle : 0.550 7.847 7920 Z= 0.276 Chirality : 0.038 0.157 947 Planarity : 0.003 0.032 984 Dihedral : 10.186 89.131 870 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.23 % Allowed : 16.44 % Favored : 81.34 % 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: 2.20 (0.31), residues: 740 helix: 2.95 (0.24), residues: 448 sheet: 0.70 (0.75), residues: 50 loop : -1.44 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 616 HIS 0.005 0.001 HIS D 342 PHE 0.016 0.001 PHE D 518 TYR 0.005 0.001 TYR A 205 ARG 0.002 0.000 ARG B 206 ********************** 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 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.658 Fit side-chains REVERT: A 8 SER cc_start: 0.8277 (m) cc_final: 0.8015 (t) REVERT: A 182 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6821 (pt0) REVERT: B 15 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.5010 (ttp-170) REVERT: B 207 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7489 (tmm) REVERT: C 349 LYS cc_start: 0.7109 (ttpt) cc_final: 0.6889 (pttp) REVERT: D 574 ILE cc_start: 0.7850 (mm) cc_final: 0.7618 (mt) outliers start: 13 outliers final: 8 residues processed: 92 average time/residue: 0.1882 time to fit residues: 22.4253 Evaluate side-chains 92 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 182 GLU 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 83 MET Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.187616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162910 restraints weight = 5777.070| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.08 r_work: 0.3673 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5839 Z= 0.250 Angle : 0.590 7.477 7920 Z= 0.298 Chirality : 0.039 0.162 947 Planarity : 0.004 0.032 984 Dihedral : 10.576 87.019 870 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.23 % Allowed : 16.44 % Favored : 81.34 % 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: 1.97 (0.31), residues: 740 helix: 2.81 (0.23), residues: 448 sheet: 0.61 (0.73), residues: 50 loop : -1.62 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 616 HIS 0.006 0.001 HIS A 195 PHE 0.016 0.001 PHE D 518 TYR 0.006 0.001 TYR A 205 ARG 0.003 0.000 ARG C 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.31 seconds wall clock time: 59 minutes 21.81 seconds (3561.81 seconds total)