Starting phenix.real_space_refine on Wed Feb 14 08:39:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/02_2024/7zo8_14843_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/02_2024/7zo8_14843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/02_2024/7zo8_14843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/02_2024/7zo8_14843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/02_2024/7zo8_14843_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/02_2024/7zo8_14843_updated.pdb" } resolution = 3.6 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= 0.004 sd= 0.120 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 2 5.49 5 S 44 5.16 5 C 5678 2.51 5 N 1582 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 307": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8952 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4437 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} Conformer: "B" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} bond proxies already assigned to first conformer: 4478 Chain: "B" Number of atoms: 4437 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} Conformer: "B" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} bond proxies already assigned to first conformer: 4478 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 9.28, per 1000 atoms: 1.04 Number of scatterers: 8952 At special positions: 0 Unit cell: (74.825, 109.675, 135.3, 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 44 16.00 P 2 15.00 O 1646 8.00 N 1582 7.00 C 5678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 3.2 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 4 sheets defined 66.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 removed outlier: 4.002A pdb=" N TYR A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 47 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 56 through 99 removed outlier: 3.625A pdb=" N MET A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 112 through 154 removed outlier: 3.616A pdb=" N MET A 134 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 156 through 203 removed outlier: 3.640A pdb=" N GLY A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 214 through 266 Proline residue: A 234 - end of helix removed outlier: 4.926A pdb=" N ASN A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP A 238 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASN A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 317 removed outlier: 3.505A pdb=" N PHE A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.890A pdb=" N HIS A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 432 removed outlier: 3.688A pdb=" N VAL A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 447 removed outlier: 3.821A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 504 through 517 removed outlier: 3.877A pdb=" N LYS A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 569 Processing helix chain 'B' and resid 2 through 16 removed outlier: 4.002A pdb=" N TYR B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 47 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 56 through 99 removed outlier: 3.624A pdb=" N MET B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 112 through 154 removed outlier: 3.616A pdb=" N MET B 134 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 156 through 203 removed outlier: 3.639A pdb=" N GLY B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N HIS B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 214 through 266 Proline residue: B 234 - end of helix removed outlier: 4.926A pdb=" N ASN B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TRP B 238 " --> pdb=" O PRO B 234 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASN B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 317 removed outlier: 3.504A pdb=" N PHE B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 382 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.889A pdb=" N HIS B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 432 removed outlier: 3.689A pdb=" N VAL B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY B 432 " --> pdb=" O ASN B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 447 removed outlier: 3.822A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 474 through 488 Processing helix chain 'B' and resid 504 through 517 removed outlier: 3.877A pdb=" N LYS B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 569 Processing sheet with id= A, first strand: chain 'A' and resid 391 through 394 removed outlier: 5.363A pdb=" N VAL A 354 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 546 through 551 removed outlier: 3.699A pdb=" N VAL A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE A 541 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL A 539 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 391 through 394 removed outlier: 5.363A pdb=" N VAL B 354 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 546 through 551 removed outlier: 3.701A pdb=" N VAL B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE B 541 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL B 539 " --> pdb=" O SER B 550 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1730 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1470 1.31 - 1.43: 2282 1.43 - 1.55: 5262 1.55 - 1.68: 4 1.68 - 1.80: 86 Bond restraints: 9104 Sorted by residual: bond pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CB PLC B 601 " pdb=" O3 PLC B 601 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 1.332 1.416 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C' PLC B 601 " pdb=" O2 PLC B 601 " ideal model delta sigma weight residual 1.332 1.415 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" N PLC A 601 " pdb=" C5 PLC A 601 " ideal model delta sigma weight residual 1.508 1.450 0.058 2.00e-02 2.50e+03 8.35e+00 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.65: 114 105.65 - 112.72: 5050 112.72 - 119.80: 2895 119.80 - 126.88: 4173 126.88 - 133.96: 86 Bond angle restraints: 12318 Sorted by residual: angle pdb=" O1P PLC A 601 " pdb=" P PLC A 601 " pdb=" O2P PLC A 601 " ideal model delta sigma weight residual 119.61 100.95 18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" O1P PLC B 601 " pdb=" P PLC B 601 " pdb=" O2P PLC B 601 " ideal model delta sigma weight residual 119.61 101.00 18.61 3.00e+00 1.11e-01 3.85e+01 angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 110.31 -16.69 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P PLC B 601 " pdb=" P PLC B 601 " pdb=" O4P PLC B 601 " ideal model delta sigma weight residual 93.62 110.28 -16.66 3.00e+00 1.11e-01 3.09e+01 angle pdb=" C ARG A 135 " pdb=" N GLN A 136 " pdb=" CA GLN A 136 " ideal model delta sigma weight residual 120.58 114.67 5.91 1.71e+00 3.42e-01 1.20e+01 ... (remaining 12313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.06: 5159 27.06 - 54.11: 283 54.11 - 81.17: 36 81.17 - 108.23: 6 108.23 - 135.28: 6 Dihedral angle restraints: 5490 sinusoidal: 2184 harmonic: 3306 Sorted by residual: dihedral pdb=" CA SER A 50 " pdb=" C SER A 50 " pdb=" N ASP A 51 " pdb=" CA ASP A 51 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA SER B 50 " pdb=" C SER B 50 " pdb=" N ASP B 51 " pdb=" CA ASP B 51 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" C3 PLC B 601 " pdb=" C1 PLC B 601 " pdb=" C2 PLC B 601 " pdb=" O3P PLC B 601 " ideal model delta sinusoidal sigma weight residual 67.16 -157.56 -135.28 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 968 0.035 - 0.069: 349 0.069 - 0.104: 79 0.104 - 0.139: 34 0.139 - 0.174: 10 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA PRO A 103 " pdb=" N PRO A 103 " pdb=" C PRO A 103 " pdb=" CB PRO A 103 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA PRO B 103 " pdb=" N PRO B 103 " pdb=" C PRO B 103 " pdb=" CB PRO B 103 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA HIS B 137 " pdb=" N HIS B 137 " pdb=" C HIS B 137 " pdb=" CB HIS B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1437 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 134 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C MET B 134 " -0.061 2.00e-02 2.50e+03 pdb=" O MET B 134 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 135 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 134 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C MET A 134 " 0.061 2.00e-02 2.50e+03 pdb=" O MET A 134 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 135 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 359 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.26e+00 pdb=" N PRO B 360 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 360 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 360 " 0.032 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1896 2.79 - 3.31: 9288 3.31 - 3.84: 14504 3.84 - 4.37: 15560 4.37 - 4.90: 28207 Nonbonded interactions: 69455 Sorted by model distance: nonbonded pdb=" OG SER A 490 " pdb=" O ILE A 492 " model vdw 2.257 2.440 nonbonded pdb=" OG SER B 490 " pdb=" O ILE B 492 " model vdw 2.258 2.440 nonbonded pdb=" O GLY B 561 " pdb=" OG SER B 564 " model vdw 2.319 2.440 nonbonded pdb=" O GLY A 561 " pdb=" OG SER A 564 " model vdw 2.319 2.440 nonbonded pdb=" NH2 ARG A 423 " pdb=" OE2 GLU B 217 " model vdw 2.346 2.520 ... (remaining 69450 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 87 or resid 89 through 116 or resid 118 through \ 570 or resid 601)) selection = (chain 'B' and (resid 1 through 87 or resid 89 through 116 or resid 118 through \ 570 or resid 601)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 3.440 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 33.890 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 0.087 9104 Z= 0.279 Angle : 0.704 18.665 12318 Z= 0.336 Chirality : 0.041 0.174 1440 Planarity : 0.004 0.057 1572 Dihedral : 16.849 135.282 3350 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.75 % Favored : 94.89 % Rotamer: Outliers : 0.42 % Allowed : 0.21 % Favored : 99.36 % 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: 1.72 (0.26), residues: 1140 helix: 2.12 (0.19), residues: 782 sheet: 0.61 (0.58), residues: 70 loop : -1.58 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.005 0.001 HIS B 137 PHE 0.018 0.001 PHE A 195 TYR 0.007 0.001 TYR A 461 ARG 0.007 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.085 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1622 time to fit residues: 27.3359 Evaluate side-chains 90 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.4980 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.0030 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9104 Z= 0.172 Angle : 0.531 8.292 12318 Z= 0.275 Chirality : 0.040 0.163 1440 Planarity : 0.004 0.041 1572 Dihedral : 12.163 131.223 1320 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.14 % Favored : 95.51 % Rotamer: Outliers : 1.27 % Allowed : 6.16 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1140 helix: 2.17 (0.19), residues: 784 sheet: 0.63 (0.57), residues: 70 loop : -1.65 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.004 0.001 HIS B 137 PHE 0.017 0.001 PHE A 195 TYR 0.022 0.001 TYR A 263 ARG 0.002 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.996 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.2191 time to fit residues: 34.0063 Evaluate side-chains 96 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 422 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 0.0050 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 overall best weight: 0.4912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9104 Z= 0.167 Angle : 0.525 7.306 12318 Z= 0.269 Chirality : 0.039 0.162 1440 Planarity : 0.004 0.037 1572 Dihedral : 11.192 115.371 1320 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.17 % Allowed : 8.92 % Favored : 89.92 % 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: 1.81 (0.26), residues: 1140 helix: 2.21 (0.19), residues: 784 sheet: 0.64 (0.57), residues: 70 loop : -1.61 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS B 137 PHE 0.016 0.001 PHE A 195 TYR 0.022 0.001 TYR A 263 ARG 0.004 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.076 Fit side-chains REVERT: A 263 TYR cc_start: 0.8335 (t80) cc_final: 0.8108 (t80) REVERT: B 263 TYR cc_start: 0.8357 (t80) cc_final: 0.8033 (t80) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.1696 time to fit residues: 23.5777 Evaluate side-chains 92 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.0980 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 110 optimal weight: 0.0980 chunk 54 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9104 Z= 0.195 Angle : 0.533 6.947 12318 Z= 0.272 Chirality : 0.040 0.160 1440 Planarity : 0.004 0.035 1572 Dihedral : 10.127 92.425 1320 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 1.59 % Allowed : 9.24 % Favored : 89.17 % 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: 1.79 (0.26), residues: 1140 helix: 2.20 (0.19), residues: 784 sheet: 0.57 (0.56), residues: 70 loop : -1.62 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 106 HIS 0.005 0.001 HIS A 137 PHE 0.019 0.001 PHE A 68 TYR 0.020 0.001 TYR A 263 ARG 0.001 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.996 Fit side-chains REVERT: A 393 MET cc_start: 0.6740 (tpp) cc_final: 0.6378 (tpp) REVERT: B 393 MET cc_start: 0.6747 (tpp) cc_final: 0.6402 (tpp) outliers start: 11 outliers final: 9 residues processed: 93 average time/residue: 0.1680 time to fit residues: 23.9783 Evaluate side-chains 95 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 94 optimal weight: 0.0000 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9104 Z= 0.217 Angle : 0.544 8.542 12318 Z= 0.278 Chirality : 0.040 0.163 1440 Planarity : 0.004 0.036 1572 Dihedral : 9.497 75.255 1320 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.31 % Favored : 95.33 % Rotamer: Outliers : 1.38 % Allowed : 10.72 % Favored : 87.90 % 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: 1.81 (0.26), residues: 1140 helix: 2.19 (0.19), residues: 784 sheet: 0.76 (0.58), residues: 70 loop : -1.61 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 238 HIS 0.006 0.001 HIS B 137 PHE 0.015 0.001 PHE A 195 TYR 0.024 0.001 TYR B 263 ARG 0.001 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.928 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 96 average time/residue: 0.1651 time to fit residues: 24.3094 Evaluate side-chains 97 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 0.0470 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9104 Z= 0.188 Angle : 0.537 7.904 12318 Z= 0.270 Chirality : 0.039 0.160 1440 Planarity : 0.003 0.036 1572 Dihedral : 8.901 63.329 1320 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.79 % Favored : 95.86 % Rotamer: Outliers : 1.80 % Allowed : 11.68 % Favored : 86.52 % 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: 1.87 (0.26), residues: 1140 helix: 2.25 (0.19), residues: 784 sheet: 0.80 (0.58), residues: 70 loop : -1.62 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.005 0.001 HIS A 137 PHE 0.016 0.001 PHE B 195 TYR 0.024 0.001 TYR A 263 ARG 0.002 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.059 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1678 time to fit residues: 25.0203 Evaluate side-chains 96 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9104 Z= 0.196 Angle : 0.542 8.256 12318 Z= 0.272 Chirality : 0.039 0.158 1440 Planarity : 0.003 0.037 1572 Dihedral : 8.568 58.457 1320 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.31 % Favored : 95.33 % Rotamer: Outliers : 1.70 % Allowed : 12.42 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.26), residues: 1140 helix: 2.28 (0.19), residues: 782 sheet: 0.79 (0.59), residues: 70 loop : -1.65 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 106 HIS 0.005 0.001 HIS A 137 PHE 0.015 0.001 PHE A 195 TYR 0.024 0.001 TYR B 263 ARG 0.002 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.071 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 96 average time/residue: 0.1680 time to fit residues: 24.8907 Evaluate side-chains 97 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9104 Z= 0.212 Angle : 0.551 8.890 12318 Z= 0.277 Chirality : 0.039 0.159 1440 Planarity : 0.003 0.036 1572 Dihedral : 8.470 59.936 1320 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.14 % Favored : 95.51 % Rotamer: Outliers : 1.80 % Allowed : 12.42 % Favored : 85.77 % 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: 1.89 (0.26), residues: 1140 helix: 2.28 (0.19), residues: 782 sheet: 0.79 (0.59), residues: 70 loop : -1.63 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 106 HIS 0.006 0.001 HIS B 137 PHE 0.015 0.001 PHE B 195 TYR 0.024 0.001 TYR A 263 ARG 0.002 0.000 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.110 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 96 average time/residue: 0.1703 time to fit residues: 24.9798 Evaluate side-chains 97 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 0.0770 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9104 Z= 0.182 Angle : 0.540 9.770 12318 Z= 0.269 Chirality : 0.039 0.159 1440 Planarity : 0.003 0.036 1572 Dihedral : 8.216 59.975 1320 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 1.49 % Allowed : 12.95 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.26), residues: 1140 helix: 2.34 (0.19), residues: 782 sheet: 0.78 (0.60), residues: 70 loop : -1.60 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.005 0.001 HIS A 137 PHE 0.015 0.001 PHE B 195 TYR 0.022 0.001 TYR B 263 ARG 0.002 0.000 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.961 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 95 average time/residue: 0.1704 time to fit residues: 24.9339 Evaluate side-chains 99 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9104 Z= 0.238 Angle : 0.570 9.444 12318 Z= 0.285 Chirality : 0.040 0.160 1440 Planarity : 0.004 0.037 1572 Dihedral : 8.145 58.043 1320 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 1.59 % Allowed : 12.85 % Favored : 85.56 % 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: 1.87 (0.26), residues: 1140 helix: 2.26 (0.19), residues: 782 sheet: 0.69 (0.59), residues: 70 loop : -1.61 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.006 0.001 HIS A 137 PHE 0.016 0.001 PHE B 195 TYR 0.022 0.001 TYR A 263 ARG 0.003 0.000 ARG B 288 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.033 Fit side-chains REVERT: A 393 MET cc_start: 0.6649 (tpp) cc_final: 0.6258 (tpp) outliers start: 11 outliers final: 11 residues processed: 92 average time/residue: 0.1696 time to fit residues: 23.8835 Evaluate side-chains 98 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS B 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.206418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154787 restraints weight = 27105.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.154990 restraints weight = 33915.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.151980 restraints weight = 14207.583| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9104 Z= 0.234 Angle : 0.568 10.131 12318 Z= 0.285 Chirality : 0.040 0.162 1440 Planarity : 0.004 0.037 1572 Dihedral : 8.110 57.668 1320 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.31 % Favored : 95.33 % Rotamer: Outliers : 1.59 % Allowed : 13.16 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.26), residues: 1140 helix: 2.23 (0.19), residues: 782 sheet: 0.67 (0.59), residues: 70 loop : -1.60 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.006 0.001 HIS B 137 PHE 0.016 0.001 PHE B 195 TYR 0.023 0.001 TYR B 263 ARG 0.003 0.000 ARG B 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1721.90 seconds wall clock time: 32 minutes 12.39 seconds (1932.39 seconds total)