Starting phenix.real_space_refine on Wed Feb 14 02:12:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2024/7z2g_14465_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2024/7z2g_14465.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2024/7z2g_14465_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2024/7z2g_14465_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2024/7z2g_14465_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2024/7z2g_14465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2024/7z2g_14465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2024/7z2g_14465_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2024/7z2g_14465_updated.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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: 7 Type Number sf(0) Gaussians P 35 5.49 5 S 14 5.16 5 Cl 1 4.86 5 C 5323 2.51 5 N 1401 2.21 5 O 1629 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 89": "OE1" <-> "OE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8406 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4324 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 499} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3333 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 30, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2KW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.13, per 1000 atoms: 0.61 Number of scatterers: 8406 At special positions: 0 Unit cell: (98.94, 109.61, 97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 14 16.00 P 35 15.00 F 3 9.00 O 1629 8.00 N 1401 7.00 C 5323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.5 seconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 10 sheets defined 34.1% alpha, 12.8% beta 13 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 33 through 44 removed outlier: 4.177A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.593A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N TYR A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 127' Processing helix chain 'A' and resid 156 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.666A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 269 removed outlier: 4.257A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.872A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 364 through 382 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.769A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.762A pdb=" N GLU A 546 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 551 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.695A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.765A pdb=" N LYS B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 174 removed outlier: 3.976A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.698A pdb=" N ARG B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.573A pdb=" N HIS B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 395 through 399 Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.673A pdb=" N GLN A 145 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 143 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 105 through 110 Processing sheet with id= C, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= D, first strand: chain 'A' and resid 326 through 331 removed outlier: 3.898A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 340 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 389 through 391 Processing sheet with id= F, first strand: chain 'A' and resid 464 through 470 removed outlier: 4.373A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR A 497 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA A 534 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 60 through 63 Processing sheet with id= H, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.554A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 129 through 132 Processing sheet with id= J, first strand: chain 'B' and resid 414 through 416 removed outlier: 5.996A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1316 1.27 - 1.40: 2137 1.40 - 1.54: 5024 1.54 - 1.67: 193 1.67 - 1.81: 26 Bond restraints: 8696 Sorted by residual: bond pdb=" C10 2KW A 601 " pdb=" C9 2KW A 601 " ideal model delta sigma weight residual 1.354 1.522 -0.168 2.00e-02 2.50e+03 7.04e+01 bond pdb=" C2 OMC E 4 " pdb=" N3 OMC E 4 " ideal model delta sigma weight residual 1.491 1.344 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" C21 2KW A 601 " pdb=" N20 2KW A 601 " ideal model delta sigma weight residual 1.356 1.499 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" C2 OMC E 2 " pdb=" N3 OMC E 2 " ideal model delta sigma weight residual 1.491 1.350 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C10 2KW A 601 " pdb=" N11 2KW A 601 " ideal model delta sigma weight residual 1.355 1.489 -0.134 2.00e-02 2.50e+03 4.51e+01 ... (remaining 8691 not shown) Histogram of bond angle deviations from ideal: 94.10 - 111.00: 3607 111.00 - 127.90: 8215 127.90 - 144.80: 152 144.80 - 161.70: 0 161.70 - 178.60: 1 Bond angle restraints: 11975 Sorted by residual: angle pdb=" C ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta sigma weight residual 109.38 94.10 15.28 2.03e+00 2.43e-01 5.67e+01 angle pdb=" C CYS A 63 " pdb=" CA CYS A 63 " pdb=" CB CYS A 63 " ideal model delta sigma weight residual 109.66 120.31 -10.65 1.94e+00 2.66e-01 3.01e+01 angle pdb=" N ASP A 186 " pdb=" CA ASP A 186 " pdb=" C ASP A 186 " ideal model delta sigma weight residual 109.06 117.88 -8.82 1.70e+00 3.46e-01 2.69e+01 angle pdb=" N GLY B 155 " pdb=" CA GLY B 155 " pdb=" C GLY B 155 " ideal model delta sigma weight residual 113.86 107.18 6.68 1.50e+00 4.44e-01 1.98e+01 angle pdb=" C5' DG E 33 " pdb=" C4' DG E 33 " pdb=" O4' DG E 33 " ideal model delta sigma weight residual 109.40 115.87 -6.47 1.50e+00 4.44e-01 1.86e+01 ... (remaining 11970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 4333 17.27 - 34.55: 561 34.55 - 51.82: 161 51.82 - 69.09: 48 69.09 - 86.37: 12 Dihedral angle restraints: 5115 sinusoidal: 2364 harmonic: 2751 Sorted by residual: dihedral pdb=" C ASP A 186 " pdb=" N ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta harmonic sigma weight residual -122.60 -107.57 -15.03 0 2.50e+00 1.60e-01 3.61e+01 dihedral pdb=" CA ILE A 411 " pdb=" C ILE A 411 " pdb=" N PRO A 412 " pdb=" CA PRO A 412 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE A 77 " pdb=" C PHE A 77 " pdb=" N ARG A 78 " pdb=" CA ARG A 78 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1177 0.083 - 0.166: 111 0.166 - 0.249: 7 0.249 - 0.332: 1 0.332 - 0.415: 2 Chirality restraints: 1298 Sorted by residual: chirality pdb=" C4' DG E 32 " pdb=" C5' DG E 32 " pdb=" O4' DG E 32 " pdb=" C3' DG E 32 " both_signs ideal model delta sigma weight residual False -2.53 -2.11 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" C4' DG E 33 " pdb=" C5' DG E 33 " pdb=" O4' DG E 33 " pdb=" C3' DG E 33 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C4' DC E 22 " pdb=" C5' DC E 22 " pdb=" O4' DC E 22 " pdb=" C3' DC E 22 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1295 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 2 " 0.045 2.00e-02 2.50e+03 5.85e-01 7.69e+03 pdb=" C4' OMC E 2 " -0.479 2.00e-02 2.50e+03 pdb=" O4' OMC E 2 " -0.797 2.00e-02 2.50e+03 pdb=" C3' OMC E 2 " 0.577 2.00e-02 2.50e+03 pdb=" O3' OMC E 2 " 0.515 2.00e-02 2.50e+03 pdb=" C2' OMC E 2 " 0.260 2.00e-02 2.50e+03 pdb=" O2' OMC E 2 " -0.813 2.00e-02 2.50e+03 pdb=" C1' OMC E 2 " -0.221 2.00e-02 2.50e+03 pdb=" N1 OMC E 2 " 0.913 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 4 " 0.010 2.00e-02 2.50e+03 5.60e-01 7.05e+03 pdb=" C4' OMC E 4 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMC E 4 " 0.538 2.00e-02 2.50e+03 pdb=" C3' OMC E 4 " -0.612 2.00e-02 2.50e+03 pdb=" O3' OMC E 4 " -0.570 2.00e-02 2.50e+03 pdb=" C2' OMC E 4 " -0.185 2.00e-02 2.50e+03 pdb=" O2' OMC E 4 " 0.938 2.00e-02 2.50e+03 pdb=" C1' OMC E 4 " 0.264 2.00e-02 2.50e+03 pdb=" N1 OMC E 4 " -0.814 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 358 " 0.492 9.50e-02 1.11e+02 2.20e-01 2.97e+01 pdb=" NE ARG A 358 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 358 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 358 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 358 " 0.017 2.00e-02 2.50e+03 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2637 2.84 - 3.35: 7497 3.35 - 3.87: 13792 3.87 - 4.38: 16062 4.38 - 4.90: 26817 Nonbonded interactions: 66805 Sorted by model distance: nonbonded pdb=" O VAL A 35 " pdb=" OG1 THR A 39 " model vdw 2.324 2.440 nonbonded pdb=" O PHE A 77 " pdb=" N ASN A 81 " model vdw 2.327 2.520 nonbonded pdb=" OH TYR B 115 " pdb=" OE1 GLN B 182 " model vdw 2.360 2.440 nonbonded pdb=" OG1 THR A 107 " pdb=" NE2 HIS A 198 " model vdw 2.371 2.520 nonbonded pdb=" O LYS B 366 " pdb=" OE1 GLU B 370 " model vdw 2.382 3.040 ... (remaining 66800 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 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: 0.960 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 0.168 8696 Z= 0.439 Angle : 0.728 15.282 11975 Z= 0.409 Chirality : 0.049 0.415 1298 Planarity : 0.023 0.585 1390 Dihedral : 17.087 86.367 3339 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.24 % Allowed : 1.57 % Favored : 98.19 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.03 % 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: -0.62 (0.27), residues: 931 helix: 0.63 (0.31), residues: 316 sheet: -0.91 (0.40), residues: 151 loop : -0.91 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B 414 HIS 0.003 0.001 HIS A 315 PHE 0.011 0.001 PHE B 130 TYR 0.027 0.001 TYR A 405 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.942 Fit side-chains REVERT: A 164 MET cc_start: 0.8586 (tpp) cc_final: 0.7881 (tpp) REVERT: A 500 GLN cc_start: 0.7479 (mp10) cc_final: 0.7121 (mm-40) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.1869 time to fit residues: 31.2668 Evaluate side-chains 83 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 50.0000 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8696 Z= 0.314 Angle : 0.732 12.884 11975 Z= 0.413 Chirality : 0.044 0.179 1298 Planarity : 0.007 0.126 1390 Dihedral : 16.588 100.080 1389 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.57 % Allowed : 11.45 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.64 (0.27), residues: 931 helix: 0.62 (0.30), residues: 319 sheet: -1.02 (0.39), residues: 154 loop : -0.91 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 383 HIS 0.005 0.001 HIS A 315 PHE 0.018 0.002 PHE B 61 TYR 0.013 0.002 TYR A 405 ARG 0.002 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8619 (tpp) cc_final: 0.8079 (tpp) REVERT: A 500 GLN cc_start: 0.7551 (mp10) cc_final: 0.7152 (mt0) outliers start: 13 outliers final: 9 residues processed: 100 average time/residue: 0.1859 time to fit residues: 27.0874 Evaluate side-chains 95 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.7514 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8696 Z= 0.362 Angle : 0.749 12.988 11975 Z= 0.422 Chirality : 0.045 0.182 1298 Planarity : 0.007 0.120 1390 Dihedral : 16.712 95.586 1389 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.65 % Allowed : 14.22 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.90 (0.27), residues: 931 helix: 0.37 (0.30), residues: 325 sheet: -0.94 (0.40), residues: 147 loop : -1.15 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 383 HIS 0.006 0.001 HIS A 315 PHE 0.019 0.002 PHE B 130 TYR 0.013 0.002 TYR A 232 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.969 Fit side-chains REVERT: A 500 GLN cc_start: 0.7654 (mp10) cc_final: 0.7190 (mt0) outliers start: 22 outliers final: 15 residues processed: 105 average time/residue: 0.1822 time to fit residues: 28.0135 Evaluate side-chains 103 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8696 Z= 0.328 Angle : 0.734 12.916 11975 Z= 0.416 Chirality : 0.044 0.149 1298 Planarity : 0.006 0.120 1390 Dihedral : 16.566 92.518 1389 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.01 % Allowed : 16.39 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.93 (0.27), residues: 931 helix: 0.35 (0.30), residues: 326 sheet: -0.93 (0.40), residues: 147 loop : -1.19 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 383 HIS 0.004 0.001 HIS A 315 PHE 0.027 0.002 PHE B 87 TYR 0.012 0.002 TYR B 144 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.940 Fit side-chains REVERT: A 500 GLN cc_start: 0.7678 (mp10) cc_final: 0.7208 (mt0) outliers start: 25 outliers final: 20 residues processed: 107 average time/residue: 0.1754 time to fit residues: 27.8145 Evaluate side-chains 103 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8696 Z= 0.347 Angle : 0.734 12.815 11975 Z= 0.417 Chirality : 0.045 0.260 1298 Planarity : 0.006 0.120 1390 Dihedral : 16.553 92.302 1389 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.73 % Allowed : 17.35 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.27), residues: 931 helix: 0.34 (0.30), residues: 325 sheet: -1.07 (0.40), residues: 148 loop : -1.21 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 383 HIS 0.005 0.001 HIS A 315 PHE 0.018 0.001 PHE B 130 TYR 0.013 0.002 TYR A 232 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 85 time to evaluate : 0.925 Fit side-chains REVERT: A 376 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8426 (m) REVERT: A 500 GLN cc_start: 0.7696 (mp10) cc_final: 0.7236 (mt0) REVERT: B 346 PHE cc_start: 0.6179 (m-80) cc_final: 0.5624 (m-80) outliers start: 31 outliers final: 23 residues processed: 107 average time/residue: 0.2118 time to fit residues: 33.3573 Evaluate side-chains 107 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8696 Z= 0.217 Angle : 0.684 12.900 11975 Z= 0.394 Chirality : 0.042 0.213 1298 Planarity : 0.006 0.117 1390 Dihedral : 16.425 93.811 1389 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.25 % Allowed : 18.80 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.71 (0.28), residues: 931 helix: 0.60 (0.30), residues: 326 sheet: -1.07 (0.39), residues: 154 loop : -0.99 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 383 HIS 0.003 0.001 HIS B 208 PHE 0.024 0.001 PHE B 87 TYR 0.009 0.001 TYR B 144 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7603 (mp10) cc_final: 0.7206 (mt0) REVERT: A 511 ASP cc_start: 0.7687 (t0) cc_final: 0.7195 (t0) REVERT: B 346 PHE cc_start: 0.6063 (m-80) cc_final: 0.5554 (m-80) outliers start: 27 outliers final: 22 residues processed: 116 average time/residue: 0.1735 time to fit residues: 29.6594 Evaluate side-chains 109 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 chunk 67 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8696 Z= 0.270 Angle : 0.708 12.689 11975 Z= 0.402 Chirality : 0.043 0.196 1298 Planarity : 0.006 0.119 1390 Dihedral : 16.512 92.425 1389 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.73 % Allowed : 18.31 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.71 (0.27), residues: 931 helix: 0.64 (0.30), residues: 326 sheet: -0.94 (0.40), residues: 149 loop : -1.09 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 383 HIS 0.004 0.001 HIS A 315 PHE 0.015 0.001 PHE B 130 TYR 0.011 0.001 TYR B 144 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 85 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7615 (mp10) cc_final: 0.7201 (mt0) REVERT: A 511 ASP cc_start: 0.7683 (t0) cc_final: 0.7199 (t0) REVERT: B 346 PHE cc_start: 0.6074 (m-80) cc_final: 0.5591 (m-80) outliers start: 31 outliers final: 28 residues processed: 107 average time/residue: 0.1759 time to fit residues: 27.7534 Evaluate side-chains 107 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8696 Z= 0.248 Angle : 0.700 12.692 11975 Z= 0.399 Chirality : 0.042 0.178 1298 Planarity : 0.006 0.119 1390 Dihedral : 16.551 92.275 1389 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.61 % Allowed : 18.92 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.28), residues: 931 helix: 0.64 (0.30), residues: 328 sheet: -0.90 (0.40), residues: 149 loop : -1.03 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 383 HIS 0.003 0.001 HIS A 315 PHE 0.013 0.001 PHE B 130 TYR 0.015 0.001 TYR A 232 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8386 (m) REVERT: A 500 GLN cc_start: 0.7648 (mp10) cc_final: 0.7246 (mt0) REVERT: A 511 ASP cc_start: 0.7662 (t0) cc_final: 0.7162 (t0) REVERT: B 346 PHE cc_start: 0.6086 (m-80) cc_final: 0.5623 (m-80) outliers start: 30 outliers final: 28 residues processed: 111 average time/residue: 0.1906 time to fit residues: 30.3754 Evaluate side-chains 114 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8696 Z= 0.188 Angle : 0.678 12.757 11975 Z= 0.390 Chirality : 0.042 0.202 1298 Planarity : 0.006 0.118 1390 Dihedral : 16.458 92.731 1389 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.01 % Allowed : 19.28 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.47 (0.28), residues: 931 helix: 0.83 (0.30), residues: 328 sheet: -0.76 (0.40), residues: 149 loop : -0.97 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 383 HIS 0.003 0.001 HIS B 208 PHE 0.031 0.001 PHE B 87 TYR 0.009 0.001 TYR A 232 ARG 0.002 0.000 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8207 (tp) cc_final: 0.7959 (tt) REVERT: A 500 GLN cc_start: 0.7604 (mp10) cc_final: 0.7212 (mt0) REVERT: A 511 ASP cc_start: 0.7654 (t0) cc_final: 0.7379 (t0) REVERT: B 346 PHE cc_start: 0.6072 (m-80) cc_final: 0.5630 (m-80) outliers start: 25 outliers final: 22 residues processed: 113 average time/residue: 0.1918 time to fit residues: 31.0049 Evaluate side-chains 112 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8696 Z= 0.371 Angle : 0.755 12.500 11975 Z= 0.423 Chirality : 0.045 0.211 1298 Planarity : 0.006 0.122 1390 Dihedral : 16.726 86.604 1389 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.37 % Allowed : 19.16 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.88 (0.27), residues: 931 helix: 0.46 (0.30), residues: 329 sheet: -0.96 (0.40), residues: 147 loop : -1.19 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 383 HIS 0.005 0.001 HIS A 315 PHE 0.020 0.002 PHE B 130 TYR 0.017 0.002 TYR A 232 ARG 0.006 0.000 ARG B 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 0.869 Fit side-chains REVERT: A 210 LEU cc_start: 0.8242 (tp) cc_final: 0.7975 (tt) REVERT: A 376 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8421 (m) REVERT: A 500 GLN cc_start: 0.7723 (mp10) cc_final: 0.7329 (mt0) REVERT: B 346 PHE cc_start: 0.6118 (m-80) cc_final: 0.5645 (m-80) outliers start: 28 outliers final: 22 residues processed: 107 average time/residue: 0.1809 time to fit residues: 28.2315 Evaluate side-chains 104 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.190597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.159460 restraints weight = 9098.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.156150 restraints weight = 14948.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.157003 restraints weight = 14751.240| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8696 Z= 0.229 Angle : 0.695 12.685 11975 Z= 0.398 Chirality : 0.042 0.196 1298 Planarity : 0.006 0.119 1390 Dihedral : 16.527 87.702 1389 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.89 % Allowed : 19.76 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.28), residues: 931 helix: 0.60 (0.30), residues: 326 sheet: -0.89 (0.40), residues: 149 loop : -1.06 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 383 HIS 0.003 0.001 HIS A 315 PHE 0.012 0.001 PHE B 130 TYR 0.011 0.001 TYR A 232 ARG 0.004 0.000 ARG B 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1477.73 seconds wall clock time: 28 minutes 8.77 seconds (1688.77 seconds total)