Starting phenix.real_space_refine on Thu Mar 14 22:23:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/03_2024/8gy2_34368_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/03_2024/8gy2_34368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/03_2024/8gy2_34368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/03_2024/8gy2_34368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/03_2024/8gy2_34368_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gy2_34368/03_2024/8gy2_34368_updated.pdb" } resolution = 2.5 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= 0.017 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 S 44 5.16 5 C 6347 2.51 5 N 1674 2.21 5 O 1873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 359": "OE1" <-> "OE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "C GLU 115": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9943 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5621 Classifications: {'peptide': 723} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 676} Chain: "B" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3264 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 33, 'TRANS': 399} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 98} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {' CA': 1, 'HEC': 1, 'PQQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 165 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 5.55, per 1000 atoms: 0.56 Number of scatterers: 9943 At special positions: 0 Unit cell: (73.95, 87, 130.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 44 16.00 O 1873 8.00 N 1674 7.00 C 6347 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 122 " distance=2.03 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=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 1.8 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 12 sheets defined 26.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.850A pdb=" N ASP A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 47 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.613A pdb=" N ALA A 137 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASP A 138 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 413 through 416 No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 486 through 497 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.754A pdb=" N GLY A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY A 595 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 652 Processing helix chain 'A' and resid 654 through 657 No H-bonds generated for 'chain 'A' and resid 654 through 657' Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 679 through 686 Processing helix chain 'A' and resid 705 through 730 removed outlier: 5.113A pdb=" N ASP A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ASP A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 742 No H-bonds generated for 'chain 'A' and resid 739 through 742' Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 56 through 59 No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 122 through 128 removed outlier: 4.050A pdb=" N ALA B 127 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 165 through 174 removed outlier: 4.051A pdb=" N MET B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 199 Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 275 through 283 removed outlier: 3.832A pdb=" N ASP B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 290 through 301 Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 341 through 344 No H-bonds generated for 'chain 'B' and resid 341 through 344' Processing helix chain 'B' and resid 362 through 365 No H-bonds generated for 'chain 'B' and resid 362 through 365' Processing helix chain 'B' and resid 370 through 377 Processing helix chain 'B' and resid 403 through 414 Processing helix chain 'B' and resid 427 through 435 removed outlier: 3.510A pdb=" N THR B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'C' and resid 51 through 59 Processing helix chain 'C' and resid 70 through 79 removed outlier: 4.013A pdb=" N GLY C 75 " --> pdb=" O PRO C 71 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 96 removed outlier: 4.220A pdb=" N GLY C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 130 Processing sheet with id= A, first strand: chain 'A' and resid 99 through 101 removed outlier: 6.225A pdb=" N ASP A 118 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 124 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.739A pdb=" N ARG A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP A 177 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP A 169 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU A 175 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 206 through 209 removed outlier: 5.923A pdb=" N ASP A 226 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 232 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 282 through 285 Processing sheet with id= E, first strand: chain 'A' and resid 349 through 356 removed outlier: 5.989A pdb=" N ASP A 377 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE A 383 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 420 through 422 Processing sheet with id= G, first strand: chain 'A' and resid 436 through 438 removed outlier: 4.472A pdb=" N GLY A 501 " --> pdb=" O HIS A 519 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 515 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASP A 507 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 527 through 529 removed outlier: 6.056A pdb=" N ASP A 548 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP A 554 " --> pdb=" O ASP A 548 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 569 through 573 removed outlier: 5.504A pdb=" N SER A 613 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU A 82 " --> pdb=" O SER A 613 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 73 through 75 Processing sheet with id= K, first strand: chain 'B' and resid 380 through 382 Processing sheet with id= L, first strand: chain 'C' and resid 99 through 101 259 hydrogen bonds defined for protein. 714 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: 2.81 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 3409 1.37 - 1.53: 6392 1.53 - 1.69: 364 1.69 - 1.85: 76 1.85 - 2.01: 16 Bond restraints: 10257 Sorted by residual: bond pdb=" C2D HEC A 801 " pdb=" C3D HEC A 801 " ideal model delta sigma weight residual 1.544 1.327 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C2D HEC B 502 " pdb=" C3D HEC B 502 " ideal model delta sigma weight residual 1.544 1.328 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C2D HEC B 503 " pdb=" C3D HEC B 503 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC B 501 " pdb=" C3D HEC B 501 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CAC HEC B 503 " pdb=" CBC HEC B 503 " ideal model delta sigma weight residual 1.544 1.359 0.185 2.00e-02 2.50e+03 8.55e+01 ... (remaining 10252 not shown) Histogram of bond angle deviations from ideal: 88.60 - 106.87: 468 106.87 - 125.14: 13180 125.14 - 143.42: 377 143.42 - 161.69: 0 161.69 - 179.96: 8 Bond angle restraints: 14033 Sorted by residual: angle pdb=" C3D HEC B 502 " pdb=" CAD HEC B 502 " pdb=" CBD HEC B 502 " ideal model delta sigma weight residual 109.50 123.32 -13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" CA GLU A 36 " pdb=" CB GLU A 36 " pdb=" CG GLU A 36 " ideal model delta sigma weight residual 114.10 121.46 -7.36 2.00e+00 2.50e-01 1.36e+01 angle pdb=" C3D HEC B 503 " pdb=" CAD HEC B 503 " pdb=" CBD HEC B 503 " ideal model delta sigma weight residual 109.50 119.18 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C3D HEC B 501 " pdb=" CAD HEC B 501 " pdb=" CBD HEC B 501 " ideal model delta sigma weight residual 109.50 118.14 -8.64 3.00e+00 1.11e-01 8.29e+00 angle pdb=" C VAL A 101 " pdb=" N ASN A 102 " pdb=" CA ASN A 102 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.90e+00 ... (remaining 14028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.25: 5193 20.25 - 40.49: 540 40.49 - 60.74: 113 60.74 - 80.98: 21 80.98 - 101.23: 7 Dihedral angle restraints: 5874 sinusoidal: 2307 harmonic: 3567 Sorted by residual: dihedral pdb=" C16 U10 B 504 " pdb=" C17 U10 B 504 " pdb=" C18 U10 B 504 " pdb=" C19 U10 B 504 " ideal model delta sinusoidal sigma weight residual 199.79 98.56 101.23 1 2.00e+01 2.50e-03 2.87e+01 dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N CYS A 142 " pdb=" CA CYS A 142 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ALA B 393 " pdb=" C ALA B 393 " pdb=" N MET B 394 " pdb=" CA MET B 394 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 5871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 792 0.029 - 0.059: 391 0.059 - 0.088: 135 0.088 - 0.117: 74 0.117 - 0.146: 20 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA ILE A 349 " pdb=" N ILE A 349 " pdb=" C ILE A 349 " pdb=" CB ILE A 349 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ASN A 102 " pdb=" N ASN A 102 " pdb=" C ASN A 102 " pdb=" CB ASN A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE A 423 " pdb=" N ILE A 423 " pdb=" C ILE A 423 " pdb=" CB ILE A 423 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 1409 not shown) Planarity restraints: 1834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A PQQ A 802 " 0.002 2.00e-02 2.50e+03 2.94e-02 3.90e+01 pdb=" C2 PQQ A 802 " 0.014 2.00e-02 2.50e+03 pdb=" C2X PQQ A 802 " 0.031 2.00e-02 2.50e+03 pdb=" C3 PQQ A 802 " -0.005 2.00e-02 2.50e+03 pdb=" C3A PQQ A 802 " -0.013 2.00e-02 2.50e+03 pdb=" C4 PQQ A 802 " -0.031 2.00e-02 2.50e+03 pdb=" C5 PQQ A 802 " 0.026 2.00e-02 2.50e+03 pdb=" C6A PQQ A 802 " 0.013 2.00e-02 2.50e+03 pdb=" C7 PQQ A 802 " -0.001 2.00e-02 2.50e+03 pdb=" C7X PQQ A 802 " -0.012 2.00e-02 2.50e+03 pdb=" C8 PQQ A 802 " -0.013 2.00e-02 2.50e+03 pdb=" C9 PQQ A 802 " -0.016 2.00e-02 2.50e+03 pdb=" C9A PQQ A 802 " 0.001 2.00e-02 2.50e+03 pdb=" C9X PQQ A 802 " -0.025 2.00e-02 2.50e+03 pdb=" N1 PQQ A 802 " 0.019 2.00e-02 2.50e+03 pdb=" N6 PQQ A 802 " 0.020 2.00e-02 2.50e+03 pdb=" O4 PQQ A 802 " -0.077 2.00e-02 2.50e+03 pdb=" O5 PQQ A 802 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC B 502 " -0.027 2.00e-02 2.50e+03 5.84e-02 3.41e+01 pdb=" CGD HEC B 502 " 0.101 2.00e-02 2.50e+03 pdb=" O1D HEC B 502 " -0.036 2.00e-02 2.50e+03 pdb=" O2D HEC B 502 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC B 503 " -0.024 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" CGD HEC B 503 " 0.090 2.00e-02 2.50e+03 pdb=" O1D HEC B 503 " -0.033 2.00e-02 2.50e+03 pdb=" O2D HEC B 503 " -0.034 2.00e-02 2.50e+03 ... (remaining 1831 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 33 2.39 - 3.02: 5749 3.02 - 3.64: 15438 3.64 - 4.27: 25420 4.27 - 4.90: 41076 Nonbonded interactions: 87716 Sorted by model distance: nonbonded pdb=" O ASP A 342 " pdb=" OD1 ASP A 342 " model vdw 1.759 3.040 nonbonded pdb=" OE1 GLU B 91 " pdb=" NE2 HIS B 92 " model vdw 1.897 2.520 nonbonded pdb=" OE1 GLU B 91 " pdb=" CD2 HIS B 92 " model vdw 2.012 3.260 nonbonded pdb=" N1 PQQ A 802 " pdb=" O9B PQQ A 802 " model vdw 2.116 2.520 nonbonded pdb=" OD2 ASP A 342 " pdb=" O5 PQQ A 802 " model vdw 2.154 3.040 ... (remaining 87711 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: 2.220 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: 0.000 Extract box with map and model: 7.200 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.090 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.007 0.217 10257 Z= 0.506 Angle : 0.668 13.820 14033 Z= 0.314 Chirality : 0.043 0.146 1412 Planarity : 0.005 0.058 1834 Dihedral : 17.176 101.226 3622 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.88 % Allowed : 21.87 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.26 (0.24), residues: 1258 helix: 1.17 (0.32), residues: 292 sheet: -0.18 (0.41), residues: 152 loop : -0.68 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 331 HIS 0.002 0.000 HIS A 362 PHE 0.008 0.001 PHE C 100 TYR 0.010 0.001 TYR A 593 ARG 0.001 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 MET cc_start: 0.9067 (tpt) cc_final: 0.7857 (tpt) outliers start: 29 outliers final: 28 residues processed: 100 average time/residue: 1.1515 time to fit residues: 124.7348 Evaluate side-chains 100 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.0020 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN B 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10257 Z= 0.224 Angle : 0.584 10.417 14033 Z= 0.280 Chirality : 0.044 0.149 1412 Planarity : 0.004 0.044 1834 Dihedral : 10.367 100.888 1461 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.28 % Allowed : 20.87 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.22 (0.24), residues: 1258 helix: 1.32 (0.32), residues: 287 sheet: -0.15 (0.41), residues: 152 loop : -0.69 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.003 0.001 HIS A 756 PHE 0.009 0.001 PHE A 383 TYR 0.012 0.001 TYR A 593 ARG 0.002 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 75 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8629 (p0) cc_final: 0.8309 (t0) REVERT: A 731 GLU cc_start: 0.8145 (tt0) cc_final: 0.7863 (mt-10) REVERT: B 277 MET cc_start: 0.9274 (tpt) cc_final: 0.7271 (tpt) outliers start: 33 outliers final: 18 residues processed: 101 average time/residue: 1.0746 time to fit residues: 118.2361 Evaluate side-chains 91 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 0.0030 chunk 122 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 740 GLN B 270 HIS B 446 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10257 Z= 0.190 Angle : 0.564 11.674 14033 Z= 0.269 Chirality : 0.044 0.147 1412 Planarity : 0.004 0.042 1834 Dihedral : 10.004 100.980 1443 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.28 % Allowed : 21.07 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.18 (0.24), residues: 1258 helix: 1.28 (0.32), residues: 291 sheet: -0.15 (0.41), residues: 152 loop : -0.64 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.003 0.000 HIS B 92 PHE 0.009 0.001 PHE C 100 TYR 0.011 0.001 TYR A 593 ARG 0.001 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 76 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8612 (p0) cc_final: 0.8362 (t0) REVERT: A 731 GLU cc_start: 0.8226 (tt0) cc_final: 0.7942 (mt-10) outliers start: 33 outliers final: 18 residues processed: 103 average time/residue: 1.0686 time to fit residues: 120.2828 Evaluate side-chains 90 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.0970 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 108 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 100 optimal weight: 0.1980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 GLN B 270 HIS C 103 ASN C 123 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10257 Z= 0.143 Angle : 0.539 12.197 14033 Z= 0.256 Chirality : 0.043 0.141 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.593 99.957 1437 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.98 % Allowed : 21.27 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.12 (0.24), residues: 1258 helix: 1.41 (0.32), residues: 290 sheet: -0.18 (0.42), residues: 151 loop : -0.61 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.002 0.000 HIS B 92 PHE 0.009 0.001 PHE C 100 TYR 0.008 0.001 TYR A 374 ARG 0.001 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 77 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8555 (p0) cc_final: 0.8324 (t0) REVERT: A 731 GLU cc_start: 0.8229 (tt0) cc_final: 0.7986 (mt-10) REVERT: B 277 MET cc_start: 0.9271 (tpt) cc_final: 0.7232 (tpt) outliers start: 30 outliers final: 16 residues processed: 99 average time/residue: 1.0619 time to fit residues: 114.8715 Evaluate side-chains 91 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 64 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.0170 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 HIS C 103 ASN C 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10257 Z= 0.280 Angle : 0.620 15.344 14033 Z= 0.292 Chirality : 0.046 0.151 1412 Planarity : 0.004 0.040 1834 Dihedral : 9.750 99.955 1435 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.88 % Allowed : 21.67 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.21 (0.24), residues: 1258 helix: 1.28 (0.32), residues: 291 sheet: -0.26 (0.41), residues: 153 loop : -0.65 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 585 HIS 0.004 0.001 HIS A 756 PHE 0.010 0.001 PHE A 383 TYR 0.016 0.001 TYR A 329 ARG 0.002 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 GLU cc_start: 0.8359 (tt0) cc_final: 0.8062 (mt-10) REVERT: B 137 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8566 (ttp) REVERT: B 318 GLN cc_start: 0.8281 (mt0) cc_final: 0.7907 (mt0) outliers start: 29 outliers final: 17 residues processed: 93 average time/residue: 1.1057 time to fit residues: 112.2538 Evaluate side-chains 87 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 64 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 102 ASN B 270 HIS C 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10257 Z= 0.207 Angle : 0.582 14.313 14033 Z= 0.275 Chirality : 0.044 0.145 1412 Planarity : 0.004 0.038 1834 Dihedral : 9.670 101.179 1435 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.58 % Allowed : 21.87 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.21 (0.24), residues: 1258 helix: 1.31 (0.32), residues: 291 sheet: -0.25 (0.41), residues: 153 loop : -0.65 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.003 0.000 HIS A 756 PHE 0.009 0.001 PHE C 100 TYR 0.012 0.001 TYR A 593 ARG 0.001 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.9090 (mtp) REVERT: B 318 GLN cc_start: 0.8309 (mt0) cc_final: 0.7939 (mt0) outliers start: 26 outliers final: 19 residues processed: 91 average time/residue: 1.1339 time to fit residues: 112.3995 Evaluate side-chains 91 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 120 optimal weight: 0.0020 chunk 75 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10257 Z= 0.159 Angle : 0.550 12.804 14033 Z= 0.260 Chirality : 0.043 0.143 1412 Planarity : 0.004 0.036 1834 Dihedral : 9.457 100.885 1435 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.49 % Allowed : 21.87 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.12 (0.24), residues: 1258 helix: 1.42 (0.32), residues: 290 sheet: -0.25 (0.41), residues: 153 loop : -0.60 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 331 HIS 0.002 0.000 HIS A 756 PHE 0.010 0.001 PHE C 100 TYR 0.009 0.001 TYR A 593 ARG 0.001 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 71 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7857 (t160) cc_final: 0.7548 (t0) REVERT: B 178 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.9064 (mtp) REVERT: B 318 GLN cc_start: 0.8291 (mt0) cc_final: 0.7911 (mt0) outliers start: 25 outliers final: 17 residues processed: 90 average time/residue: 1.0426 time to fit residues: 102.5236 Evaluate side-chains 87 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 64 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN B 270 HIS C 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10257 Z= 0.178 Angle : 0.567 14.427 14033 Z= 0.264 Chirality : 0.043 0.144 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.445 100.543 1434 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.19 % Allowed : 22.47 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.10 (0.24), residues: 1258 helix: 1.41 (0.32), residues: 290 sheet: -0.25 (0.41), residues: 153 loop : -0.57 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.002 0.000 HIS A 756 PHE 0.009 0.001 PHE C 100 TYR 0.011 0.001 TYR A 593 ARG 0.001 0.000 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8389 (p0) REVERT: A 76 ASN cc_start: 0.7908 (t160) cc_final: 0.7581 (t0) REVERT: B 84 THR cc_start: 0.8580 (m) cc_final: 0.8127 (p) REVERT: B 178 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.9080 (mtp) REVERT: B 318 GLN cc_start: 0.8294 (mt0) cc_final: 0.7894 (mt0) outliers start: 22 outliers final: 16 residues processed: 88 average time/residue: 1.1242 time to fit residues: 107.9452 Evaluate side-chains 88 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 73 optimal weight: 0.0770 chunk 118 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10257 Z= 0.180 Angle : 0.573 14.691 14033 Z= 0.265 Chirality : 0.043 0.143 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.433 100.533 1434 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.99 % Allowed : 22.66 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.10 (0.24), residues: 1258 helix: 1.32 (0.32), residues: 295 sheet: -0.26 (0.41), residues: 153 loop : -0.54 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.002 0.000 HIS A 756 PHE 0.009 0.001 PHE C 100 TYR 0.011 0.001 TYR A 593 ARG 0.001 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7898 (t160) cc_final: 0.7579 (t0) REVERT: B 84 THR cc_start: 0.8604 (m) cc_final: 0.8068 (p) REVERT: B 178 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.9049 (mtt) REVERT: B 318 GLN cc_start: 0.8298 (mt0) cc_final: 0.7896 (mt0) REVERT: C 115 GLU cc_start: 0.8704 (tt0) cc_final: 0.8451 (tt0) outliers start: 20 outliers final: 15 residues processed: 90 average time/residue: 1.1651 time to fit residues: 114.0669 Evaluate side-chains 86 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 0.0770 chunk 124 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS B 446 ASN C 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10257 Z= 0.187 Angle : 0.582 14.697 14033 Z= 0.269 Chirality : 0.043 0.146 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.205 100.532 1431 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.69 % Allowed : 22.96 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.09 (0.24), residues: 1258 helix: 1.32 (0.32), residues: 295 sheet: -0.26 (0.41), residues: 153 loop : -0.53 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.002 0.000 HIS A 756 PHE 0.009 0.001 PHE C 100 TYR 0.011 0.001 TYR A 593 ARG 0.001 0.000 ARG A 598 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7871 (t160) cc_final: 0.7550 (t0) REVERT: B 84 THR cc_start: 0.8593 (m) cc_final: 0.8096 (p) REVERT: B 178 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.9052 (mtt) REVERT: B 277 MET cc_start: 0.9234 (tpt) cc_final: 0.7061 (tpt) REVERT: B 318 GLN cc_start: 0.8306 (mt0) cc_final: 0.7912 (mt0) REVERT: C 115 GLU cc_start: 0.8702 (tt0) cc_final: 0.8449 (tt0) outliers start: 17 outliers final: 15 residues processed: 86 average time/residue: 1.1457 time to fit residues: 107.0815 Evaluate side-chains 85 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.069784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.056358 restraints weight = 19527.640| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.17 r_work: 0.2577 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10257 Z= 0.211 Angle : 0.596 15.114 14033 Z= 0.273 Chirality : 0.044 0.147 1412 Planarity : 0.004 0.037 1834 Dihedral : 9.271 100.854 1431 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.89 % Allowed : 22.86 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.12 (0.24), residues: 1258 helix: 1.30 (0.32), residues: 295 sheet: -0.27 (0.41), residues: 153 loop : -0.55 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 585 HIS 0.008 0.001 HIS B 92 PHE 0.008 0.001 PHE C 100 TYR 0.012 0.001 TYR A 329 ARG 0.001 0.000 ARG A 671 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3024.64 seconds wall clock time: 54 minutes 28.64 seconds (3268.64 seconds total)