Starting phenix.real_space_refine on Sun Feb 18 12:45:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc3_23268/02_2024/7lc3_23268_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc3_23268/02_2024/7lc3_23268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc3_23268/02_2024/7lc3_23268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc3_23268/02_2024/7lc3_23268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc3_23268/02_2024/7lc3_23268_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc3_23268/02_2024/7lc3_23268_trim_updated.pdb" } resolution = 3.23 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= 0.001 sd= 0.093 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: 8 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 6984 2.51 5 N 1824 2.21 5 O 1979 1.98 5 H 11144 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21999 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8444 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 10173 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 26, 'TRANS': 646} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 2848 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 13, 'TRANS': 174} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 421 Classifications: {'peptide': 27} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {' MG': 1, '9Y0': 1, 'ACP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 11.20, per 1000 atoms: 0.51 Number of scatterers: 21999 At special positions: 0 Unit cell: (73.485, 111.78, 157.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 2 19.00 S 61 16.00 P 4 15.00 Mg 1 11.99 O 1979 8.00 N 1824 7.00 C 6984 6.00 H 11144 1.00 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: 20.81 Conformation dependent library (CDL) restraints added in 2.5 seconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 7 sheets defined 58.0% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 40 through 50 removed outlier: 4.117A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 133 through 156 Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.299A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 367 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 Processing helix chain 'A' and resid 411 through 437 removed outlier: 4.298A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.559A pdb=" N ALA A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 508 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 525 through 548 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'B' and resid 11 through 23 Processing helix chain 'B' and resid 27 through 30 No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 34 through 55 removed outlier: 3.511A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 100 removed outlier: 3.700A pdb=" N GLN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 199 through 207 removed outlier: 3.627A pdb=" N MET B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 246 removed outlier: 3.852A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 285 removed outlier: 4.939A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 3.776A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 367 through 370 No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'B' and resid 398 through 407 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.524A pdb=" N ALA B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 555 through 594 removed outlier: 3.938A pdb=" N LEU B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 566 " --> pdb=" O HIS B 563 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 613 through 637 removed outlier: 4.366A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 679 removed outlier: 3.905A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 662 " --> pdb=" O GLY B 658 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 5 through 33 removed outlier: 4.494A pdb=" N TYR C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 3 through 24 Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 106 through 109 Processing sheet with id= C, first strand: chain 'B' and resid 131 through 134 removed outlier: 6.296A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 150 through 153 Processing sheet with id= E, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= F, first strand: chain 'B' and resid 466 through 470 removed outlier: 7.186A pdb=" N VAL B 531 " --> pdb=" O MET B 515 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLY B 517 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL B 533 " --> pdb=" O GLY B 517 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 322 through 324 removed outlier: 7.110A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1656 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: 8.82 Time building geometry restraints manager: 19.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 11132 1.01 - 1.21: 15 1.21 - 1.42: 4353 1.42 - 1.62: 6572 1.62 - 1.82: 114 Bond restraints: 22186 Sorted by residual: bond pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 1.333 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" O3A ACP B 803 " pdb=" PB ACP B 803 " ideal model delta sigma weight residual 1.698 1.596 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O2A ACP B 803 " pdb=" PA ACP B 803 " ideal model delta sigma weight residual 1.505 1.605 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O2B ACP B 803 " pdb=" PB ACP B 803 " ideal model delta sigma weight residual 1.507 1.603 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 9Y0 B 801 " pdb=" O7 9Y0 B 801 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.04e+01 ... (remaining 22181 not shown) Histogram of bond angle deviations from ideal: 77.77 - 89.24: 4 89.24 - 100.71: 27 100.71 - 112.17: 26200 112.17 - 123.64: 12292 123.64 - 135.10: 1707 Bond angle restraints: 40230 Sorted by residual: angle pdb=" HB1 ALA B 498 " pdb=" CB ALA B 498 " pdb=" HB3 ALA B 498 " ideal model delta sigma weight residual 110.00 77.77 32.23 3.00e+00 1.11e-01 1.15e+02 angle pdb=" HB2 ALA B 498 " pdb=" CB ALA B 498 " pdb=" HB3 ALA B 498 " ideal model delta sigma weight residual 110.00 78.94 31.06 3.00e+00 1.11e-01 1.07e+02 angle pdb=" CA ALA B 498 " pdb=" CB ALA B 498 " pdb=" HB2 ALA B 498 " ideal model delta sigma weight residual 109.00 81.70 27.30 3.00e+00 1.11e-01 8.28e+01 angle pdb=" CA ALA B 498 " pdb=" CB ALA B 498 " pdb=" HB1 ALA B 498 " ideal model delta sigma weight residual 109.00 84.13 24.87 3.00e+00 1.11e-01 6.88e+01 angle pdb=" HB1 ALA B 498 " pdb=" CB ALA B 498 " pdb=" HB2 ALA B 498 " ideal model delta sigma weight residual 110.00 133.66 -23.66 3.00e+00 1.11e-01 6.22e+01 ... (remaining 40225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 9684 24.54 - 49.08: 512 49.08 - 73.62: 188 73.62 - 98.16: 14 98.16 - 122.69: 2 Dihedral angle restraints: 10400 sinusoidal: 5743 harmonic: 4657 Sorted by residual: dihedral pdb=" O1B ACP B 803 " pdb=" C3B ACP B 803 " pdb=" PB ACP B 803 " pdb=" PG ACP B 803 " ideal model delta sinusoidal sigma weight residual -52.82 69.87 -122.69 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C27 9Y0 B 801 " pdb=" C28 9Y0 B 801 " pdb=" C29 9Y0 B 801 " pdb=" C30 9Y0 B 801 " ideal model delta sinusoidal sigma weight residual -178.88 -62.49 -116.39 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C ALA C 73 " pdb=" N ALA C 73 " pdb=" CA ALA C 73 " pdb=" CB ALA C 73 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 10397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1392 0.071 - 0.141: 352 0.141 - 0.211: 56 0.211 - 0.282: 4 0.282 - 0.352: 2 Chirality restraints: 1806 Sorted by residual: chirality pdb=" CA ALA C 73 " pdb=" N ALA C 73 " pdb=" C ALA C 73 " pdb=" CB ALA C 73 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA TRP A 176 " pdb=" N TRP A 176 " pdb=" C TRP A 176 " pdb=" CB TRP A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB VAL A 508 " pdb=" CA VAL A 508 " pdb=" CG1 VAL A 508 " pdb=" CG2 VAL A 508 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1803 not shown) Planarity restraints: 3275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 606 " 0.068 2.00e-02 2.50e+03 8.96e-02 1.20e+02 pdb=" CG ASN B 606 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 606 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 606 " -0.143 2.00e-02 2.50e+03 pdb="HD21 ASN B 606 " -0.019 2.00e-02 2.50e+03 pdb="HD22 ASN B 606 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 239 " 0.065 2.00e-02 2.50e+03 8.40e-02 1.06e+02 pdb=" CG ASN A 239 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 239 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 239 " -0.134 2.00e-02 2.50e+03 pdb="HD21 ASN A 239 " -0.014 2.00e-02 2.50e+03 pdb="HD22 ASN A 239 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 361 " 0.051 2.00e-02 2.50e+03 7.52e-02 8.49e+01 pdb=" CG ASN B 361 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN B 361 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN B 361 " -0.122 2.00e-02 2.50e+03 pdb="HD21 ASN B 361 " -0.023 2.00e-02 2.50e+03 pdb="HD22 ASN B 361 " 0.124 2.00e-02 2.50e+03 ... (remaining 3272 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.30: 4813 2.30 - 3.01: 63453 3.01 - 3.72: 85724 3.72 - 4.43: 132226 4.43 - 5.14: 205286 Nonbonded interactions: 491502 Sorted by model distance: nonbonded pdb=" O ASN B 361 " pdb="HD21 ASN B 361 " model vdw 1.591 1.850 nonbonded pdb=" O ARG C 68 " pdb=" HH TYR C 77 " model vdw 1.632 1.850 nonbonded pdb=" H THR A 401 " pdb=" OD2 ASP B 300 " model vdw 1.638 1.850 nonbonded pdb=" OD1 ASP B 143 " pdb=" H GLY B 178 " model vdw 1.678 1.850 nonbonded pdb=" O THR A 105 " pdb=" HG SER A 108 " model vdw 1.682 1.850 ... (remaining 491497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 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: 0.430 Extract box with map and model: 9.090 Check model and map are aligned: 0.330 Set scattering table: 0.090 Process input model: 81.300 Find NCS groups from input model: 0.490 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: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.012 0.209 11042 Z= 0.791 Angle : 1.154 18.724 15024 Z= 0.627 Chirality : 0.063 0.352 1806 Planarity : 0.007 0.075 1898 Dihedral : 15.226 122.695 3966 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.12 % Allowed : 10.53 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.20), residues: 1437 helix: -0.72 (0.16), residues: 877 sheet: -1.95 (0.46), residues: 88 loop : -2.16 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 115 HIS 0.012 0.003 HIS B 404 PHE 0.022 0.003 PHE A 149 TYR 0.040 0.005 TYR A 126 ARG 0.009 0.001 ARG B 651 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 240 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8898 (mtt) cc_final: 0.8670 (mtp) REVERT: A 412 ARG cc_start: 0.7228 (tmm-80) cc_final: 0.6573 (ttt90) REVERT: B 125 GLN cc_start: 0.7162 (tt0) cc_final: 0.6932 (tp40) REVERT: B 318 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7400 (tt0) REVERT: B 530 ASP cc_start: 0.7143 (t70) cc_final: 0.6745 (t0) REVERT: B 570 MET cc_start: 0.8418 (mmt) cc_final: 0.7924 (mmt) REVERT: B 647 SER cc_start: 0.8546 (m) cc_final: 0.8279 (p) outliers start: 24 outliers final: 10 residues processed: 259 average time/residue: 0.6250 time to fit residues: 219.2483 Evaluate side-chains 155 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain D residue 10 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 111 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 128 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN B 26 ASN B 653 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11042 Z= 0.188 Angle : 0.547 6.261 15024 Z= 0.283 Chirality : 0.039 0.145 1806 Planarity : 0.004 0.051 1898 Dihedral : 9.316 90.103 1612 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.42 % Allowed : 11.68 % Favored : 86.90 % 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: -0.70 (0.21), residues: 1437 helix: 0.31 (0.17), residues: 870 sheet: -1.83 (0.46), residues: 90 loop : -1.49 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 245 HIS 0.003 0.001 HIS B 404 PHE 0.014 0.001 PHE A 47 TYR 0.019 0.001 TYR A 381 ARG 0.003 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8685 (tpp) cc_final: 0.8409 (mmm) REVERT: B 318 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7404 (tt0) REVERT: B 647 SER cc_start: 0.8353 (m) cc_final: 0.8122 (p) REVERT: B 649 MET cc_start: 0.8470 (tpp) cc_final: 0.8222 (tpt) outliers start: 16 outliers final: 8 residues processed: 170 average time/residue: 0.5233 time to fit residues: 130.2899 Evaluate side-chains 139 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 564 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 0.0270 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11042 Z= 0.215 Angle : 0.518 5.472 15024 Z= 0.269 Chirality : 0.039 0.151 1806 Planarity : 0.004 0.042 1898 Dihedral : 8.490 82.067 1604 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.88 % Allowed : 12.48 % Favored : 86.64 % 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: -0.07 (0.21), residues: 1437 helix: 0.81 (0.17), residues: 870 sheet: -1.53 (0.49), residues: 90 loop : -1.26 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 245 HIS 0.003 0.001 HIS A 451 PHE 0.010 0.001 PHE A 149 TYR 0.021 0.001 TYR A 381 ARG 0.002 0.000 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8601 (tpp) cc_final: 0.8213 (mtp) REVERT: B 318 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7403 (tt0) REVERT: B 455 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8160 (tm-30) REVERT: B 647 SER cc_start: 0.8408 (m) cc_final: 0.8121 (p) REVERT: B 649 MET cc_start: 0.8275 (tpp) cc_final: 0.7583 (tpt) outliers start: 10 outliers final: 5 residues processed: 139 average time/residue: 0.5052 time to fit residues: 100.2575 Evaluate side-chains 127 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 393 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 0.0870 chunk 86 optimal weight: 0.0010 chunk 129 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11042 Z= 0.146 Angle : 0.472 4.940 15024 Z= 0.241 Chirality : 0.038 0.138 1806 Planarity : 0.004 0.038 1898 Dihedral : 7.908 85.295 1600 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.53 % Allowed : 13.10 % Favored : 86.37 % 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: 0.39 (0.22), residues: 1437 helix: 1.19 (0.17), residues: 878 sheet: -1.27 (0.50), residues: 90 loop : -1.15 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 245 HIS 0.002 0.001 HIS A 451 PHE 0.008 0.001 PHE B 457 TYR 0.020 0.001 TYR A 381 ARG 0.003 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8522 (tpp) cc_final: 0.8147 (mtp) REVERT: B 47 THR cc_start: 0.8127 (t) cc_final: 0.7690 (m) REVERT: B 318 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7444 (tt0) REVERT: B 455 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 647 SER cc_start: 0.8363 (m) cc_final: 0.8092 (p) REVERT: B 649 MET cc_start: 0.8247 (tpp) cc_final: 0.7702 (tpt) REVERT: C 161 LYS cc_start: 0.8682 (tttt) cc_final: 0.8458 (tttm) outliers start: 6 outliers final: 6 residues processed: 137 average time/residue: 0.4877 time to fit residues: 98.1673 Evaluate side-chains 135 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 393 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11042 Z= 0.234 Angle : 0.493 6.022 15024 Z= 0.254 Chirality : 0.038 0.137 1806 Planarity : 0.004 0.039 1898 Dihedral : 7.710 86.865 1600 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.06 % Allowed : 13.01 % Favored : 85.93 % 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: 0.49 (0.22), residues: 1437 helix: 1.23 (0.17), residues: 885 sheet: -1.32 (0.50), residues: 96 loop : -1.02 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 245 HIS 0.002 0.001 HIS A 451 PHE 0.011 0.001 PHE A 149 TYR 0.020 0.001 TYR A 381 ARG 0.002 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8565 (tpp) cc_final: 0.8251 (mtp) REVERT: B 318 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7501 (tt0) REVERT: B 455 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8111 (tm-30) REVERT: B 647 SER cc_start: 0.8407 (m) cc_final: 0.8120 (p) REVERT: B 649 MET cc_start: 0.8164 (tpp) cc_final: 0.7615 (tpt) REVERT: C 161 LYS cc_start: 0.8708 (tttt) cc_final: 0.8447 (tttm) outliers start: 12 outliers final: 11 residues processed: 138 average time/residue: 0.4857 time to fit residues: 99.0019 Evaluate side-chains 137 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 574 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11042 Z= 0.190 Angle : 0.470 5.223 15024 Z= 0.241 Chirality : 0.038 0.135 1806 Planarity : 0.004 0.042 1898 Dihedral : 7.270 77.317 1599 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.97 % Allowed : 13.19 % Favored : 85.84 % 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: 0.66 (0.22), residues: 1437 helix: 1.35 (0.18), residues: 878 sheet: -1.30 (0.50), residues: 96 loop : -0.89 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 245 HIS 0.003 0.001 HIS A 451 PHE 0.012 0.001 PHE A 109 TYR 0.020 0.001 TYR A 381 ARG 0.001 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8563 (tpp) cc_final: 0.8259 (mtp) REVERT: B 47 THR cc_start: 0.8127 (t) cc_final: 0.7726 (m) REVERT: B 318 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7532 (tt0) REVERT: B 455 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8089 (tm-30) REVERT: B 647 SER cc_start: 0.8392 (m) cc_final: 0.8131 (p) REVERT: B 649 MET cc_start: 0.8135 (tpp) cc_final: 0.7615 (tpt) outliers start: 11 outliers final: 10 residues processed: 137 average time/residue: 0.4834 time to fit residues: 98.2088 Evaluate side-chains 131 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 574 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 100 optimal weight: 0.2980 chunk 77 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11042 Z= 0.169 Angle : 0.460 6.352 15024 Z= 0.236 Chirality : 0.037 0.136 1806 Planarity : 0.003 0.042 1898 Dihedral : 6.883 70.322 1599 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.15 % Allowed : 13.36 % Favored : 85.49 % 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: 0.85 (0.22), residues: 1437 helix: 1.52 (0.18), residues: 872 sheet: -1.34 (0.51), residues: 94 loop : -0.78 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 245 HIS 0.003 0.001 HIS A 451 PHE 0.011 0.001 PHE A 109 TYR 0.020 0.001 TYR A 381 ARG 0.001 0.000 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8551 (tpp) cc_final: 0.8225 (mtp) REVERT: A 397 MET cc_start: 0.7724 (mmm) cc_final: 0.7249 (mtt) REVERT: B 47 THR cc_start: 0.8038 (t) cc_final: 0.7656 (m) REVERT: B 455 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8071 (tm-30) REVERT: B 647 SER cc_start: 0.8417 (m) cc_final: 0.8100 (p) REVERT: B 649 MET cc_start: 0.8125 (tpp) cc_final: 0.7649 (tpt) outliers start: 13 outliers final: 12 residues processed: 139 average time/residue: 0.4744 time to fit residues: 97.6902 Evaluate side-chains 135 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 574 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11042 Z= 0.298 Angle : 0.516 5.448 15024 Z= 0.269 Chirality : 0.039 0.136 1806 Planarity : 0.004 0.047 1898 Dihedral : 6.771 66.370 1599 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.42 % Allowed : 13.45 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1437 helix: 1.31 (0.17), residues: 885 sheet: -1.31 (0.52), residues: 94 loop : -0.77 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 PHE 0.013 0.001 PHE A 149 TYR 0.019 0.002 TYR A 381 ARG 0.002 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7081 (mmt) cc_final: 0.6844 (mmt) REVERT: A 160 MET cc_start: 0.8614 (tpp) cc_final: 0.8356 (mtp) REVERT: A 397 MET cc_start: 0.7857 (mmm) cc_final: 0.7395 (mtt) REVERT: B 47 THR cc_start: 0.8114 (t) cc_final: 0.7743 (m) REVERT: B 455 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8057 (tm-30) REVERT: B 647 SER cc_start: 0.8432 (m) cc_final: 0.8099 (p) REVERT: C 72 THR cc_start: 0.8659 (m) cc_final: 0.8454 (p) outliers start: 16 outliers final: 14 residues processed: 133 average time/residue: 0.4828 time to fit residues: 94.7233 Evaluate side-chains 129 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 574 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 120 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11042 Z= 0.196 Angle : 0.479 7.772 15024 Z= 0.246 Chirality : 0.038 0.135 1806 Planarity : 0.004 0.044 1898 Dihedral : 6.590 64.530 1599 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.42 % Allowed : 14.07 % Favored : 84.51 % 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: 0.85 (0.22), residues: 1437 helix: 1.44 (0.18), residues: 874 sheet: -1.26 (0.52), residues: 94 loop : -0.61 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 245 HIS 0.003 0.001 HIS A 451 PHE 0.008 0.001 PHE A 149 TYR 0.020 0.001 TYR A 381 ARG 0.002 0.000 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7056 (mmt) cc_final: 0.6848 (mmt) REVERT: A 160 MET cc_start: 0.8564 (tpp) cc_final: 0.8278 (mtp) REVERT: A 325 SER cc_start: 0.8620 (m) cc_final: 0.8300 (m) REVERT: B 47 THR cc_start: 0.8067 (t) cc_final: 0.7720 (m) REVERT: B 380 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7758 (mp10) REVERT: B 455 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8024 (tm-30) REVERT: B 647 SER cc_start: 0.8423 (m) cc_final: 0.8091 (p) outliers start: 16 outliers final: 14 residues processed: 133 average time/residue: 0.4682 time to fit residues: 92.3861 Evaluate side-chains 130 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 574 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 120 optimal weight: 0.0770 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11042 Z= 0.203 Angle : 0.479 6.622 15024 Z= 0.246 Chirality : 0.038 0.134 1806 Planarity : 0.004 0.044 1898 Dihedral : 6.431 62.987 1599 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.15 % Allowed : 13.98 % Favored : 84.87 % 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: 0.91 (0.23), residues: 1437 helix: 1.47 (0.18), residues: 873 sheet: -1.22 (0.52), residues: 94 loop : -0.57 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 245 HIS 0.003 0.001 HIS A 451 PHE 0.009 0.001 PHE A 149 TYR 0.020 0.001 TYR A 381 ARG 0.002 0.000 ARG B 511 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8554 (tpp) cc_final: 0.8271 (mtp) REVERT: A 325 SER cc_start: 0.8627 (m) cc_final: 0.8296 (m) REVERT: B 47 THR cc_start: 0.8128 (t) cc_final: 0.7800 (m) REVERT: B 380 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7795 (mp10) REVERT: B 455 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 647 SER cc_start: 0.8367 (m) cc_final: 0.8137 (p) outliers start: 13 outliers final: 13 residues processed: 129 average time/residue: 0.4965 time to fit residues: 94.9061 Evaluate side-chains 130 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 574 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111137 restraints weight = 37586.875| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.54 r_work: 0.3095 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11042 Z= 0.211 Angle : 0.482 6.639 15024 Z= 0.248 Chirality : 0.038 0.134 1806 Planarity : 0.004 0.044 1898 Dihedral : 6.305 62.362 1599 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.24 % Allowed : 13.89 % Favored : 84.87 % 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: 0.97 (0.23), residues: 1437 helix: 1.51 (0.18), residues: 869 sheet: -1.24 (0.52), residues: 94 loop : -0.48 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 245 HIS 0.003 0.001 HIS A 451 PHE 0.013 0.001 PHE B 457 TYR 0.019 0.001 TYR A 381 ARG 0.002 0.000 ARG B 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5022.62 seconds wall clock time: 90 minutes 23.42 seconds (5423.42 seconds total)