Starting phenix.real_space_refine on Fri Aug 22 16:15:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x61_38077/08_2025/8x61_38077.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x61_38077/08_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_38077/08_2025/8x61_38077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x61_38077/08_2025/8x61_38077.map" model { file = "/net/cci-nas-00/data/ceres_data/8x61_38077/08_2025/8x61_38077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x61_38077/08_2025/8x61_38077.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 3, 'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 4, 'HIS:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1} 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: {'ASN:plan1': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 4, 'TYR:plan': 1, 'ASP:plan': 1} 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: 1.33, per 1000 atoms: 0.23 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: 0.44 Conformation dependent library (CDL) restraints added in 218.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.10 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: 0.80 Time building geometry restraints manager: 0.62 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 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: 3.730 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.410 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.570 ------------------------------------------------------------------------------- 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= 0.181 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG C 533 TYR 0.006 0.001 TYR A 205 PHE 0.010 0.001 PHE D 518 TRP 0.011 0.001 TRP C 616 HIS 0.008 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5839) covalent geometry : angle 0.60439 ( 7920) hydrogen bonds : bond 0.21964 ( 385) hydrogen bonds : angle 6.09163 ( 1122) *********************** 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 : 0.197 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.0760 time to fit residues: 7.7296 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 : 0.171 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.185626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.159979 restraints weight = 5707.533| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.10 r_work: 0.3633 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5839 Z= 0.241 Angle : 0.697 9.289 7920 Z= 0.350 Chirality : 0.042 0.169 947 Planarity : 0.005 0.069 984 Dihedral : 11.533 89.517 875 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.57 % Allowed : 12.67 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.30), residues: 740 helix: 1.94 (0.23), residues: 446 sheet: -0.02 (0.66), residues: 50 loop : -1.60 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 202 TYR 0.009 0.002 TYR C 339 PHE 0.018 0.002 PHE D 518 TRP 0.013 0.002 TRP C 616 HIS 0.013 0.002 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 5839) covalent geometry : angle 0.69679 ( 7920) hydrogen bonds : bond 0.06312 ( 385) hydrogen bonds : angle 4.18742 ( 1122) *********************** 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 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.203 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 0.0754 time to fit residues: 9.5718 Evaluate side-chains 91 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR 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 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 D residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.0020 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.3586 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.190359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.165607 restraints weight = 5688.952| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.11 r_work: 0.3719 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5839 Z= 0.119 Angle : 0.520 7.089 7920 Z= 0.265 Chirality : 0.037 0.151 947 Planarity : 0.004 0.053 984 Dihedral : 10.507 89.539 872 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.71 % Allowed : 15.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.31), residues: 740 helix: 2.69 (0.24), residues: 446 sheet: 0.12 (0.67), residues: 62 loop : -1.62 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 533 TYR 0.005 0.001 TYR C 339 PHE 0.021 0.001 PHE D 518 TRP 0.011 0.001 TRP C 616 HIS 0.004 0.001 HIS D 342 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5839) covalent geometry : angle 0.52039 ( 7920) hydrogen bonds : bond 0.04203 ( 385) hydrogen bonds : angle 3.79892 ( 1122) *********************** 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 98 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.197 Fit side-chains REVERT: C 374 MET cc_start: 0.6566 (mtt) cc_final: 0.6270 (mtt) REVERT: D 626 HIS cc_start: 0.5862 (OUTLIER) cc_final: 0.5451 (t-90) outliers start: 10 outliers final: 7 residues processed: 97 average time/residue: 0.0607 time to fit residues: 7.8820 Evaluate side-chains 88 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 514 VAL 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 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.186446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.160921 restraints weight = 5690.066| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.12 r_work: 0.3669 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.004 0.036 5839 Z= 0.179 Angle : 0.590 7.350 7920 Z= 0.300 Chirality : 0.040 0.163 947 Planarity : 0.004 0.047 984 Dihedral : 11.041 87.216 872 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.31), residues: 740 helix: 2.56 (0.24), residues: 446 sheet: 0.29 (0.73), residues: 50 loop : -1.61 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 206 TYR 0.007 0.001 TYR C 339 PHE 0.020 0.002 PHE D 518 TRP 0.011 0.001 TRP C 616 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 5839) covalent geometry : angle 0.59015 ( 7920) hydrogen bonds : bond 0.04944 ( 385) hydrogen bonds : angle 3.83864 ( 1122) *********************** 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 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.214 Fit side-chains REVERT: B 15 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.5411 (ttp-170) REVERT: B 83 MET cc_start: 0.8551 (tpt) cc_final: 0.8140 (tpp) REVERT: B 212 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6919 (t0) REVERT: C 374 MET cc_start: 0.6541 (mtt) cc_final: 0.6294 (mtt) REVERT: C 526 ARG cc_start: 0.7296 (tpt170) cc_final: 0.6919 (mmt180) REVERT: D 574 ILE cc_start: 0.7989 (mm) cc_final: 0.7718 (mt) outliers start: 18 outliers final: 12 residues processed: 94 average time/residue: 0.0761 time to fit residues: 9.2146 Evaluate side-chains 92 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 576 VAL Chi-restraints excluded: chain D residue 360 MET 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 67 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.185342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.154840 restraints weight = 5753.727| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.32 r_work: 0.3643 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2020 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= 0.155 Angle : 0.568 9.169 7920 Z= 0.287 Chirality : 0.039 0.159 947 Planarity : 0.004 0.042 984 Dihedral : 10.661 87.404 870 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.08 % Allowed : 16.61 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.31), residues: 740 helix: 2.65 (0.24), residues: 448 sheet: 0.15 (0.69), residues: 62 loop : -1.74 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 206 TYR 0.005 0.001 TYR D 339 PHE 0.020 0.001 PHE D 518 TRP 0.011 0.001 TRP C 616 HIS 0.005 0.001 HIS D 342 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 5839) covalent geometry : angle 0.56834 ( 7920) hydrogen bonds : bond 0.04472 ( 385) hydrogen bonds : angle 3.74603 ( 1122) *********************** 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 98 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.141 Fit side-chains REVERT: A 195 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6582 (p-80) REVERT: B 15 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5120 (ttp-170) REVERT: B 212 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6896 (t0) REVERT: C 374 MET cc_start: 0.6433 (mtt) cc_final: 0.6225 (mtt) REVERT: C 526 ARG cc_start: 0.7238 (tpt170) cc_final: 0.6902 (mmt180) REVERT: D 574 ILE cc_start: 0.7937 (mm) cc_final: 0.7699 (mt) outliers start: 18 outliers final: 10 residues processed: 94 average time/residue: 0.0672 time to fit residues: 8.1652 Evaluate side-chains 92 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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 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 D residue 514 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.0270 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.188944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.164239 restraints weight = 5706.808| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.10 r_work: 0.3706 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5839 Z= 0.123 Angle : 0.525 7.118 7920 Z= 0.269 Chirality : 0.038 0.162 947 Planarity : 0.003 0.037 984 Dihedral : 10.349 84.995 870 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.08 % Allowed : 16.44 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.31), residues: 740 helix: 2.83 (0.24), residues: 448 sheet: 0.32 (0.70), residues: 62 loop : -1.67 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 533 TYR 0.004 0.001 TYR D 339 PHE 0.018 0.001 PHE D 518 TRP 0.010 0.001 TRP C 616 HIS 0.005 0.001 HIS D 342 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5839) covalent geometry : angle 0.52457 ( 7920) hydrogen bonds : bond 0.03937 ( 385) hydrogen bonds : angle 3.66442 ( 1122) *********************** 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 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.152 Fit side-chains REVERT: B 15 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.5051 (ttp-170) REVERT: B 207 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7565 (tmm) REVERT: B 212 ASP cc_start: 0.7093 (m-30) cc_final: 0.6859 (t0) REVERT: C 526 ARG cc_start: 0.7339 (tpt170) cc_final: 0.7007 (mmt180) REVERT: D 574 ILE cc_start: 0.7843 (mm) cc_final: 0.7587 (mt) outliers start: 18 outliers final: 9 residues processed: 97 average time/residue: 0.0660 time to fit residues: 8.1967 Evaluate side-chains 90 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 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 207 MET Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.186554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.161739 restraints weight = 5755.168| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.09 r_work: 0.3675 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5839 Z= 0.159 Angle : 0.574 7.233 7920 Z= 0.290 Chirality : 0.039 0.173 947 Planarity : 0.003 0.035 984 Dihedral : 10.744 86.125 870 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.60 % Allowed : 17.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.31), residues: 740 helix: 2.68 (0.24), residues: 448 sheet: 0.18 (0.69), residues: 62 loop : -1.73 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 206 TYR 0.006 0.001 TYR C 339 PHE 0.017 0.001 PHE D 518 TRP 0.010 0.001 TRP C 616 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5839) covalent geometry : angle 0.57366 ( 7920) hydrogen bonds : bond 0.04483 ( 385) hydrogen bonds : angle 3.76541 ( 1122) *********************** 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 103 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.123 Fit side-chains REVERT: B 15 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.5181 (ttp-170) REVERT: B 207 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7475 (tmm) REVERT: C 526 ARG cc_start: 0.7385 (tpt170) cc_final: 0.7054 (mmt180) REVERT: D 571 LEU cc_start: 0.8037 (mt) cc_final: 0.7812 (mp) REVERT: D 574 ILE cc_start: 0.7826 (mm) cc_final: 0.7599 (mt) outliers start: 21 outliers final: 13 residues processed: 95 average time/residue: 0.0623 time to fit residues: 7.6320 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 : 0.167 ------------------------------------------------------------------------------- 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 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 361 VAL Chi-restraints excluded: chain C residue 506 SER 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 44 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.187712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162965 restraints weight = 5708.648| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.09 r_work: 0.3682 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5839 Z= 0.139 Angle : 0.553 7.154 7920 Z= 0.282 Chirality : 0.038 0.178 947 Planarity : 0.003 0.033 984 Dihedral : 10.513 85.059 870 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.74 % Allowed : 18.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.31), residues: 740 helix: 2.77 (0.24), residues: 448 sheet: 0.23 (0.69), residues: 62 loop : -1.78 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 206 TYR 0.005 0.001 TYR D 339 PHE 0.016 0.001 PHE D 518 TRP 0.010 0.001 TRP C 616 HIS 0.005 0.001 HIS D 342 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5839) covalent geometry : angle 0.55345 ( 7920) hydrogen bonds : bond 0.04119 ( 385) hydrogen bonds : angle 3.71643 ( 1122) *********************** 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 98 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.131 Fit side-chains REVERT: B 15 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5200 (ttp-170) REVERT: B 207 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7417 (tmm) REVERT: D 574 ILE cc_start: 0.7857 (mm) cc_final: 0.7633 (mt) outliers start: 16 outliers final: 13 residues processed: 93 average time/residue: 0.0768 time to fit residues: 9.0725 Evaluate side-chains 97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 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 506 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.188637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.161913 restraints weight = 5752.097| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.50 r_work: 0.3651 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5839 Z= 0.128 Angle : 0.546 7.098 7920 Z= 0.278 Chirality : 0.038 0.185 947 Planarity : 0.003 0.033 984 Dihedral : 10.363 85.563 870 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.74 % Allowed : 18.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.31), residues: 740 helix: 2.81 (0.24), residues: 448 sheet: 0.34 (0.70), residues: 62 loop : -1.79 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 206 TYR 0.004 0.001 TYR D 339 PHE 0.015 0.001 PHE D 518 TRP 0.009 0.001 TRP C 616 HIS 0.003 0.001 HIS D 629 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5839) covalent geometry : angle 0.54562 ( 7920) hydrogen bonds : bond 0.03942 ( 385) hydrogen bonds : angle 3.71238 ( 1122) *********************** 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 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.158 Fit side-chains REVERT: B 15 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5138 (ttp-170) REVERT: B 207 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7571 (tmm) REVERT: D 574 ILE cc_start: 0.7829 (mm) cc_final: 0.7565 (mt) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.0746 time to fit residues: 8.5843 Evaluate side-chains 92 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 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 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 361 VAL 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 4 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.188340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.161984 restraints weight = 5809.184| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.29 r_work: 0.3666 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5839 Z= 0.135 Angle : 0.558 7.230 7920 Z= 0.283 Chirality : 0.039 0.191 947 Planarity : 0.003 0.032 984 Dihedral : 10.397 86.141 870 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.23 % Allowed : 19.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.31), residues: 740 helix: 2.76 (0.24), residues: 448 sheet: 0.41 (0.70), residues: 62 loop : -1.79 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 206 TYR 0.004 0.001 TYR A 205 PHE 0.015 0.001 PHE D 518 TRP 0.009 0.001 TRP C 616 HIS 0.003 0.001 HIS D 629 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5839) covalent geometry : angle 0.55779 ( 7920) hydrogen bonds : bond 0.04022 ( 385) hydrogen bonds : angle 3.72869 ( 1122) ********************** 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 91 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.215 Fit side-chains REVERT: B 15 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5205 (ttp-170) REVERT: B 207 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7535 (tmm) REVERT: D 513 MET cc_start: 0.3959 (ptp) cc_final: 0.3539 (ptp) REVERT: D 526 ARG cc_start: 0.7379 (tpt-90) cc_final: 0.6956 (ttm-80) REVERT: D 574 ILE cc_start: 0.7872 (mm) cc_final: 0.7615 (mt) outliers start: 13 outliers final: 11 residues processed: 87 average time/residue: 0.0782 time to fit residues: 8.7251 Evaluate side-chains 91 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 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 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 361 VAL 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 10 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.185787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160608 restraints weight = 5700.986| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.10 r_work: 0.3637 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2417 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= 0.170 Angle : 0.605 8.645 7920 Z= 0.305 Chirality : 0.040 0.189 947 Planarity : 0.004 0.033 984 Dihedral : 10.845 85.042 870 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.74 % Allowed : 18.32 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.31), residues: 740 helix: 2.60 (0.24), residues: 448 sheet: 0.63 (0.75), residues: 50 loop : -1.69 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 206 TYR 0.007 0.001 TYR A 205 PHE 0.015 0.002 PHE D 518 TRP 0.011 0.001 TRP C 616 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 5839) covalent geometry : angle 0.60484 ( 7920) hydrogen bonds : bond 0.04618 ( 385) hydrogen bonds : angle 3.82741 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1404.86 seconds wall clock time: 24 minutes 39.17 seconds (1479.17 seconds total)