Starting phenix.real_space_refine on Mon Jun 24 23:12:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/06_2024/8x61_38077_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/06_2024/8x61_38077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/06_2024/8x61_38077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/06_2024/8x61_38077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/06_2024/8x61_38077_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x61_38077/06_2024/8x61_38077_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 32 5.16 5 C 3679 2.51 5 N 1009 2.21 5 O 1011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 4.43, per 1000 atoms: 0.77 Number of scatterers: 5737 At special positions: 0 Unit cell: (72.24, 75.6, 107.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 6 15.00 O 1011 8.00 N 1009 7.00 C 3679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.2 seconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 5 sheets defined 58.9% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 74 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 96 through 107 Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 111 through 124 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 140 through 151 Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.162A pdb=" N VAL A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 74 through 80 removed outlier: 4.293A pdb=" N GLN B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 107 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 111 through 124 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 140 through 151 Processing helix chain 'B' and resid 170 through 186 removed outlier: 4.149A pdb=" N VAL B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'C' and resid 335 through 379 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) Proline residue: C 352 - end of helix 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 507 through 531 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) Processing helix chain 'C' and resid 533 through 542 Processing helix chain 'C' and resid 546 through 578 Proline residue: C 552 - end of helix Processing helix chain 'C' and resid 601 through 627 Processing helix chain 'D' and resid 335 through 350 removed outlier: 3.864A pdb=" N TYR D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 378 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 503 through 542 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) removed outlier: 5.252A pdb=" N ASP D 534 " --> pdb=" O PHE D 530 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) 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 546 through 578 Proline residue: D 552 - end of helix Processing helix chain 'D' and resid 601 through 629 removed outlier: 4.355A pdb=" N HIS D 629 " --> pdb=" O GLN D 625 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 23 through 25 Processing sheet with id= B, first strand: chain 'A' and resid 214 through 216 removed outlier: 4.220A pdb=" N THR A 209 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 206 " --> pdb=" O MET A 30 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 190 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU A 33 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N MET A 192 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N GLY A 35 " --> pdb=" O MET A 192 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 23 through 25 Processing sheet with id= D, first strand: chain 'B' and resid 214 through 216 removed outlier: 4.244A pdb=" N THR B 209 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B 206 " --> pdb=" O MET B 30 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 190 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU B 33 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET B 192 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLY B 35 " --> pdb=" O MET B 192 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 7 through 9 removed outlier: 7.431A pdb=" N LYS B 9 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN B 19 " --> pdb=" O LYS B 9 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 996 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: 1.73 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 995 1.32 - 1.45: 1408 1.45 - 1.57: 3370 1.57 - 1.69: 10 1.69 - 1.81: 56 Bond restraints: 5839 Sorted by residual: bond pdb=" C PRO D 369 " pdb=" O PRO D 369 " ideal model delta sigma weight residual 1.238 1.202 0.036 1.33e-02 5.65e+03 7.28e+00 bond pdb=" N LEU D 368 " pdb=" CA LEU D 368 " ideal model delta sigma weight residual 1.463 1.481 -0.018 6.90e-03 2.10e+04 6.52e+00 bond pdb=" O5' ATP B 301 " pdb=" PA ATP B 301 " ideal model delta sigma weight residual 1.579 1.602 -0.023 1.10e-02 8.26e+03 4.47e+00 bond pdb=" O5' ATP A 301 " pdb=" PA ATP A 301 " ideal model delta sigma weight residual 1.579 1.600 -0.021 1.10e-02 8.26e+03 3.77e+00 bond pdb=" O2B ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 1.529 1.488 0.041 2.20e-02 2.07e+03 3.49e+00 ... (remaining 5834 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.18: 146 106.18 - 113.17: 3297 113.17 - 120.15: 1976 120.15 - 127.13: 2433 127.13 - 134.11: 68 Bond angle restraints: 7920 Sorted by residual: angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 133.08 6.79 1.00e+00 1.00e+00 4.61e+01 angle pdb=" PB ATP A 301 " pdb=" O3B ATP A 301 " pdb=" PG ATP A 301 " ideal model delta sigma weight residual 139.87 133.91 5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" CA PRO D 552 " pdb=" N PRO D 552 " pdb=" CD PRO D 552 " ideal model delta sigma weight residual 112.00 106.28 5.72 1.40e+00 5.10e-01 1.67e+01 angle pdb=" N THR B 165 " pdb=" CA THR B 165 " pdb=" C THR B 165 " ideal model delta sigma weight residual 114.75 110.18 4.57 1.26e+00 6.30e-01 1.31e+01 angle pdb=" C ASP B 87 " pdb=" N HIS B 88 " pdb=" CA HIS B 88 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.52e+00 ... (remaining 7915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3105 17.96 - 35.91: 263 35.91 - 53.87: 100 53.87 - 71.82: 12 71.82 - 89.78: 9 Dihedral angle restraints: 3489 sinusoidal: 1349 harmonic: 2140 Sorted by residual: dihedral pdb=" CB GLU A 29 " pdb=" CG GLU A 29 " pdb=" CD GLU A 29 " pdb=" OE1 GLU A 29 " ideal model delta sinusoidal sigma weight residual 0.00 89.78 -89.78 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA HIS A 195 " pdb=" C HIS A 195 " pdb=" N ASP A 196 " pdb=" CA ASP A 196 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CB MET C 360 " pdb=" CG MET C 360 " pdb=" SD MET C 360 " pdb=" CE MET C 360 " ideal model delta sinusoidal sigma weight residual -180.00 -123.41 -56.59 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 717 0.040 - 0.079: 179 0.079 - 0.119: 38 0.119 - 0.158: 10 0.158 - 0.198: 3 Chirality restraints: 947 Sorted by residual: chirality pdb=" C2' ATP B 301 " pdb=" C1' ATP B 301 " pdb=" C3' ATP B 301 " pdb=" O2' ATP B 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.48 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C2' ATP A 301 " pdb=" C1' ATP A 301 " pdb=" C3' ATP A 301 " pdb=" O2' ATP A 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.50 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA ILE B 102 " pdb=" N ILE B 102 " pdb=" C ILE B 102 " pdb=" CB ILE B 102 " both_signs ideal model delta sigma weight residual False 2.43 2.27 0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 944 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 551 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO D 552 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO D 552 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 552 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 367 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C THR D 367 " 0.028 2.00e-02 2.50e+03 pdb=" O THR D 367 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU D 368 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 631 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO C 632 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 632 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 632 " -0.019 5.00e-02 4.00e+02 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 795 2.75 - 3.29: 5426 3.29 - 3.83: 9191 3.83 - 4.36: 10994 4.36 - 4.90: 19081 Nonbonded interactions: 45487 Sorted by model distance: nonbonded pdb=" O ASP A 169 " pdb=" OG SER A 173 " model vdw 2.218 2.440 nonbonded pdb=" NE2 GLN A 86 " pdb=" OD1 ASN B 167 " model vdw 2.230 2.520 nonbonded pdb=" ND2 ASN A 184 " pdb=" O VAL A 188 " model vdw 2.232 2.520 nonbonded pdb=" OE2 GLU A 181 " pdb=" OH TYR A 205 " model vdw 2.242 2.440 nonbonded pdb=" O ASN A 198 " pdb=" NH1 ARG A 202 " model vdw 2.295 2.520 ... (remaining 45482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 through 71 or (resid 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 through 196 or (resid 197 thro \ ugh 198 and (name N or name CA or name C or name O or name CB )) or resid 199 th \ rough 216 or resid 301)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 334 through 379 or resid 502 through 630 or (resid 631 and \ (name N or name CA or name C or name O or name CB )) or resid 632)) selection = (chain 'D' and (resid 334 through 341 or (resid 342 and (name N or name CA or na \ me C or name O or name CB )) or resid 343 through 345 or (resid 346 through 347 \ and (name N or name CA or name C or name O or name CB )) or resid 348 through 35 \ 2 or (resid 353 through 354 and (name N or name CA or name C or name O or name C \ B )) or resid 355 through 379 or (resid 502 through 505 and (name N or name CA o \ r name C or name O or name CB )) or resid 506 through 533 or (resid 534 and (nam \ e N or name CA or name C or name O or name CB )) or resid 535 through 576 or (re \ sid 577 through 578 and (name N or name CA or name C or name O or name CB )) or \ resid 579 or (resid 597 and (name N or name CA or name C or name O or name CB )) \ or resid 598 or (resid 599 through 600 and (name N or name CA or name C or name \ O or name CB )) or resid 601 through 602 or (resid 603 and (name N or name CA o \ r name C or name O or name CB )) or resid 604 or (resid 605 and (name N or name \ CA or name C or name O or name CB )) or resid 606 through 632)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 9.800 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.360 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.760 ------------------------------------------------------------------------------- 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= 0.253 Angle : 0.604 7.946 7920 Z= 0.333 Chirality : 0.039 0.198 947 Planarity : 0.005 0.110 984 Dihedral : 15.998 89.776 2109 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.34 % Allowed : 12.16 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.30), residues: 740 helix: 1.42 (0.24), residues: 447 sheet: -0.44 (0.62), residues: 50 loop : -1.33 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 616 HIS 0.008 0.001 HIS A 195 PHE 0.010 0.001 PHE D 518 TYR 0.006 0.001 TYR A 205 ARG 0.003 0.000 ARG C 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.584 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.2007 time to fit residues: 20.4587 Evaluate side-chains 78 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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: 3.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 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: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0987 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= 0.252 Angle : 0.572 7.259 7920 Z= 0.290 Chirality : 0.038 0.156 947 Planarity : 0.004 0.067 984 Dihedral : 10.931 89.311 875 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.88 % Allowed : 13.18 % Favored : 84.93 % 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: 1.19 (0.30), residues: 740 helix: 2.13 (0.24), residues: 445 sheet: -0.41 (0.64), residues: 62 loop : -1.61 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 616 HIS 0.010 0.001 HIS A 195 PHE 0.018 0.002 PHE D 518 TYR 0.007 0.001 TYR C 339 ARG 0.004 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 97 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.644 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 90 average time/residue: 0.1825 time to fit residues: 21.4964 Evaluate side-chains 89 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.0170 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5839 Z= 0.209 Angle : 0.527 7.202 7920 Z= 0.266 Chirality : 0.037 0.158 947 Planarity : 0.004 0.053 984 Dihedral : 10.762 89.120 872 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.60 % Allowed : 14.04 % Favored : 82.36 % 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: 1.51 (0.31), residues: 740 helix: 2.45 (0.24), residues: 445 sheet: -0.27 (0.65), residues: 62 loop : -1.63 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 616 HIS 0.008 0.001 HIS A 195 PHE 0.022 0.001 PHE D 518 TYR 0.005 0.001 TYR D 339 ARG 0.003 0.000 ARG C 533 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.565 Fit side-chains REVERT: D 626 HIS cc_start: 0.5972 (OUTLIER) cc_final: 0.5666 (t-90) outliers start: 21 outliers final: 14 residues processed: 103 average time/residue: 0.1736 time to fit residues: 23.4759 Evaluate side-chains 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 626 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.3980 chunk 50 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 71 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS D 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5839 Z= 0.157 Angle : 0.495 7.115 7920 Z= 0.255 Chirality : 0.037 0.154 947 Planarity : 0.003 0.044 984 Dihedral : 10.295 87.595 872 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.91 % Allowed : 16.10 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.31), residues: 740 helix: 2.72 (0.24), residues: 439 sheet: -0.13 (0.67), residues: 62 loop : -1.56 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 616 HIS 0.005 0.001 HIS D 342 PHE 0.021 0.001 PHE D 518 TYR 0.004 0.001 TYR D 339 ARG 0.003 0.000 ARG C 533 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.622 Fit side-chains REVERT: B 15 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.5216 (ttp-170) REVERT: C 526 ARG cc_start: 0.7241 (tpt170) cc_final: 0.6905 (mmt180) outliers start: 17 outliers final: 9 residues processed: 99 average time/residue: 0.1848 time to fit residues: 23.7258 Evaluate side-chains 92 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 173 SER 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 209 THR 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 59 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS C 539 GLN D 342 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5839 Z= 0.236 Angle : 0.553 8.770 7920 Z= 0.277 Chirality : 0.038 0.161 947 Planarity : 0.003 0.040 984 Dihedral : 10.471 86.275 870 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.11 % Allowed : 14.55 % 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: 1.58 (0.31), residues: 740 helix: 2.56 (0.24), residues: 439 sheet: -0.16 (0.66), residues: 62 loop : -1.64 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 616 HIS 0.007 0.001 HIS A 195 PHE 0.018 0.001 PHE D 518 TYR 0.005 0.001 TYR C 339 ARG 0.002 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.589 Fit side-chains REVERT: B 15 ARG cc_start: 0.5956 (OUTLIER) cc_final: 0.5417 (ttp-170) REVERT: B 83 MET cc_start: 0.8466 (tpt) cc_final: 0.8178 (tpp) REVERT: C 526 ARG cc_start: 0.7311 (tpt170) cc_final: 0.6967 (mmt180) REVERT: C 569 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8063 (mp) outliers start: 24 outliers final: 18 residues processed: 102 average time/residue: 0.1892 time to fit residues: 24.8711 Evaluate side-chains 103 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 569 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 59 optimal weight: 0.0020 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS D 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5839 Z= 0.193 Angle : 0.518 7.138 7920 Z= 0.264 Chirality : 0.038 0.169 947 Planarity : 0.003 0.036 984 Dihedral : 10.107 79.823 870 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.77 % Allowed : 15.07 % Favored : 81.16 % 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: 1.68 (0.31), residues: 740 helix: 2.66 (0.24), residues: 439 sheet: -0.14 (0.67), residues: 62 loop : -1.63 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 616 HIS 0.005 0.001 HIS A 195 PHE 0.017 0.001 PHE D 518 TYR 0.005 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 107 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.623 Fit side-chains REVERT: B 15 ARG cc_start: 0.5999 (OUTLIER) cc_final: 0.5385 (ttp-170) REVERT: B 83 MET cc_start: 0.8427 (tpt) cc_final: 0.7872 (tpp) REVERT: C 526 ARG cc_start: 0.7259 (tpt170) cc_final: 0.6992 (mmt180) REVERT: C 569 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8050 (mp) REVERT: D 526 ARG cc_start: 0.7280 (tpt-90) cc_final: 0.7066 (ttm-80) outliers start: 22 outliers final: 18 residues processed: 100 average time/residue: 0.1827 time to fit residues: 23.9398 Evaluate side-chains 103 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 569 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5839 Z= 0.259 Angle : 0.567 7.281 7920 Z= 0.288 Chirality : 0.039 0.170 947 Planarity : 0.003 0.035 984 Dihedral : 10.363 77.374 870 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.11 % Allowed : 15.41 % 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 (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: 1.41 (0.31), residues: 740 helix: 2.41 (0.24), residues: 439 sheet: -0.17 (0.68), residues: 62 loop : -1.71 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 616 HIS 0.007 0.001 HIS A 195 PHE 0.019 0.001 PHE D 518 TYR 0.007 0.001 TYR C 339 ARG 0.002 0.000 ARG D 532 *********************** 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 110 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.641 Fit side-chains REVERT: B 15 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5646 (ttp-170) REVERT: B 207 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7262 (tmm) REVERT: D 526 ARG cc_start: 0.7363 (tpt-90) cc_final: 0.7059 (ttm-80) outliers start: 24 outliers final: 17 residues processed: 102 average time/residue: 0.1925 time to fit residues: 25.3828 Evaluate side-chains 100 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain D residue 514 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS D 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5839 Z= 0.226 Angle : 0.545 7.173 7920 Z= 0.279 Chirality : 0.038 0.174 947 Planarity : 0.003 0.034 984 Dihedral : 10.062 74.077 870 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.60 % Allowed : 16.27 % Favored : 80.14 % 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: 1.48 (0.31), residues: 740 helix: 2.51 (0.24), residues: 438 sheet: -0.14 (0.68), residues: 62 loop : -1.74 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 616 HIS 0.005 0.001 HIS A 195 PHE 0.018 0.001 PHE D 518 TYR 0.005 0.001 TYR D 339 ARG 0.002 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.607 Fit side-chains REVERT: B 15 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.5578 (ttp-170) REVERT: B 207 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7253 (tmm) REVERT: D 526 ARG cc_start: 0.7390 (tpt-90) cc_final: 0.7084 (ttm-80) outliers start: 21 outliers final: 16 residues processed: 96 average time/residue: 0.1896 time to fit residues: 23.7070 Evaluate side-chains 97 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS B 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5839 Z= 0.242 Angle : 0.557 7.238 7920 Z= 0.284 Chirality : 0.039 0.181 947 Planarity : 0.003 0.033 984 Dihedral : 10.147 75.308 870 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.94 % Allowed : 16.44 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.31), residues: 740 helix: 2.44 (0.24), residues: 438 sheet: -0.13 (0.68), residues: 62 loop : -1.75 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 616 HIS 0.007 0.001 HIS A 195 PHE 0.017 0.001 PHE D 518 TYR 0.005 0.001 TYR D 339 ARG 0.002 0.000 ARG D 532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.570 Fit side-chains REVERT: B 15 ARG cc_start: 0.6039 (OUTLIER) cc_final: 0.5516 (ttp-170) REVERT: B 207 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7258 (tmm) REVERT: D 513 MET cc_start: 0.4130 (ptp) cc_final: 0.3814 (ptp) REVERT: D 526 ARG cc_start: 0.7427 (tpt-90) cc_final: 0.7129 (ttm-80) outliers start: 23 outliers final: 18 residues processed: 97 average time/residue: 0.1953 time to fit residues: 24.3758 Evaluate side-chains 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 5839 Z= 0.413 Angle : 0.678 7.440 7920 Z= 0.343 Chirality : 0.043 0.190 947 Planarity : 0.004 0.036 984 Dihedral : 10.964 82.214 870 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.77 % Allowed : 17.12 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.30), residues: 740 helix: 1.94 (0.24), residues: 439 sheet: -0.24 (0.71), residues: 50 loop : -1.78 (0.34), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 616 HIS 0.007 0.001 HIS A 195 PHE 0.021 0.002 PHE D 518 TYR 0.007 0.002 TYR D 339 ARG 0.003 0.001 ARG B 178 ********************** 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 104 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.625 Fit side-chains REVERT: B 207 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7241 (tmm) REVERT: D 526 ARG cc_start: 0.7350 (tpt-90) cc_final: 0.7008 (ttm-80) outliers start: 22 outliers final: 18 residues processed: 97 average time/residue: 0.2085 time to fit residues: 25.5680 Evaluate side-chains 97 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 51 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 = 0.186771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.161916 restraints weight = 5669.724| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.08 r_work: 0.3676 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5839 Z= 0.177 Angle : 0.531 7.047 7920 Z= 0.272 Chirality : 0.038 0.179 947 Planarity : 0.003 0.034 984 Dihedral : 9.826 72.996 870 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.25 % Allowed : 17.98 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.31), residues: 740 helix: 2.41 (0.24), residues: 438 sheet: -0.12 (0.69), residues: 62 loop : -1.78 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 616 HIS 0.003 0.001 HIS D 629 PHE 0.018 0.001 PHE D 518 TYR 0.004 0.001 TYR D 339 ARG 0.003 0.000 ARG A 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1546.39 seconds wall clock time: 28 minutes 14.50 seconds (1694.50 seconds total)