Starting phenix.real_space_refine on Tue Feb 13 12:58:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2024/6vrl_21370_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2024/6vrl_21370.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2024/6vrl_21370_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2024/6vrl_21370_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2024/6vrl_21370_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2024/6vrl_21370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2024/6vrl_21370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2024/6vrl_21370_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2024/6vrl_21370_updated.pdb" } resolution = 3.8 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= 0.971 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 34 5.16 5 C 4045 2.51 5 N 958 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4311 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 517} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'LMT': 1, 'NAG': 2, 'RFY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.85, per 1000 atoms: 0.63 Number of scatterers: 6141 At special positions: 0 Unit cell: (95.256, 104.328, 82.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 1 52.95 S 34 16.00 O 1103 8.00 N 958 7.00 C 4045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " 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=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 208 " " NAG A 702 " - " ASN A 217 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 5 sheets defined 46.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.740A pdb=" N LEU A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Proline residue: A 120 - end of helix removed outlier: 3.865A pdb=" N PHE A 127 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 156 through 189 removed outlier: 3.740A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 161 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.721A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 357 through 389 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 420 through 453 removed outlier: 3.764A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 4.751A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 495 Processing helix chain 'A' and resid 498 through 513 Processing helix chain 'A' and resid 518 through 529 Processing helix chain 'A' and resid 535 through 542 Processing helix chain 'A' and resid 544 through 558 removed outlier: 3.531A pdb=" N MET A 558 " --> pdb=" O CYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 4.254A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N CYS A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 604 through 610 Processing sheet with id= A, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.525A pdb=" N CYS C 43 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 91 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 105 through 110 removed outlier: 6.006A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 22 through 25 Processing sheet with id= D, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.811A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 102 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 100 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 112 through 118 removed outlier: 3.750A pdb=" N VAL B 112 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 53 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 70 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LYS B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TRP B 66 " --> pdb=" O LYS B 57 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 2681 1.40 - 1.58: 3595 1.58 - 1.75: 0 1.75 - 1.93: 49 1.93 - 2.11: 1 Bond restraints: 6326 Sorted by residual: bond pdb=" C06 RFY A 704 " pdb=" C07 RFY A 704 " ideal model delta sigma weight residual 1.512 1.576 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C04 RFY A 704 " pdb=" N03 RFY A 704 " ideal model delta sigma weight residual 1.445 1.492 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C3' LMT A 703 " pdb=" O3' LMT A 703 " ideal model delta sigma weight residual 1.404 1.362 0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" C02 RFY A 704 " pdb=" N03 RFY A 704 " ideal model delta sigma weight residual 1.450 1.492 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C7 LMT A 703 " pdb=" C8 LMT A 703 " ideal model delta sigma weight residual 1.529 1.489 0.040 2.00e-02 2.50e+03 4.02e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 184 106.95 - 113.71: 3435 113.71 - 120.48: 2531 120.48 - 127.24: 2385 127.24 - 134.01: 84 Bond angle restraints: 8619 Sorted by residual: angle pdb=" N VAL A 397 " pdb=" CA VAL A 397 " pdb=" C VAL A 397 " ideal model delta sigma weight residual 113.42 109.33 4.09 1.17e+00 7.31e-01 1.22e+01 angle pdb=" N ARG B 121 " pdb=" CA ARG B 121 " pdb=" C ARG B 121 " ideal model delta sigma weight residual 109.81 117.12 -7.31 2.21e+00 2.05e-01 1.09e+01 angle pdb=" C2 LMT A 703 " pdb=" C3 LMT A 703 " pdb=" C4 LMT A 703 " ideal model delta sigma weight residual 117.09 108.15 8.94 3.00e+00 1.11e-01 8.87e+00 angle pdb=" C10 LMT A 703 " pdb=" C9 LMT A 703 " pdb=" C8 LMT A 703 " ideal model delta sigma weight residual 116.03 107.32 8.71 3.00e+00 1.11e-01 8.43e+00 angle pdb=" C VAL B 120 " pdb=" N ARG B 121 " pdb=" CA ARG B 121 " ideal model delta sigma weight residual 121.80 128.79 -6.99 2.44e+00 1.68e-01 8.20e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 3406 22.02 - 44.05: 239 44.05 - 66.07: 25 66.07 - 88.09: 4 88.09 - 110.12: 2 Dihedral angle restraints: 3676 sinusoidal: 1462 harmonic: 2214 Sorted by residual: dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta harmonic sigma weight residual 180.00 128.14 51.86 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual 93.00 133.61 -40.61 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" C01 RFY A 704 " pdb=" C02 RFY A 704 " pdb=" N03 RFY A 704 " pdb=" C04 RFY A 704 " ideal model delta sinusoidal sigma weight residual -53.70 56.42 -110.12 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 3673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 714 0.042 - 0.083: 207 0.083 - 0.125: 41 0.125 - 0.166: 1 0.166 - 0.208: 3 Chirality restraints: 966 Sorted by residual: chirality pdb=" C4' LMT A 703 " pdb=" C3' LMT A 703 " pdb=" C5' LMT A 703 " pdb=" O1B LMT A 703 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C3B LMT A 703 " pdb=" C2B LMT A 703 " pdb=" C4B LMT A 703 " pdb=" O3B LMT A 703 " both_signs ideal model delta sigma weight residual False 2.50 2.29 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C5' LMT A 703 " pdb=" C4' LMT A 703 " pdb=" C6' LMT A 703 " pdb=" O5' LMT A 703 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 963 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 121 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO B 122 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 465 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C PHE A 465 " 0.034 2.00e-02 2.50e+03 pdb=" O PHE A 465 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 466 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 589 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 590 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 590 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 590 " 0.017 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.72: 265 2.72 - 3.28: 6934 3.28 - 3.84: 11086 3.84 - 4.40: 13089 4.40 - 4.96: 22141 Nonbonded interactions: 53515 Sorted by model distance: nonbonded pdb=" OG1 THR C 83 " pdb=" O THR C 94 " model vdw 2.159 2.440 nonbonded pdb=" OG SER B 110 " pdb=" O LEU B 134 " model vdw 2.173 2.440 nonbonded pdb=" O THR A 221 " pdb=" OG SER A 224 " model vdw 2.202 2.440 nonbonded pdb=" O ASP C 102 " pdb=" OH TYR C 106 " model vdw 2.235 2.440 nonbonded pdb=" O SER A 559 " pdb=" O6' LMT A 703 " model vdw 2.267 2.440 ... (remaining 53510 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: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 13.630 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.610 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 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 : 0.003 0.064 6326 Z= 0.218 Angle : 0.614 8.936 8619 Z= 0.322 Chirality : 0.040 0.208 966 Planarity : 0.004 0.067 1048 Dihedral : 14.288 110.118 2261 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -3.12 (0.27), residues: 758 helix: -0.96 (0.24), residues: 360 sheet: -3.12 (0.42), residues: 99 loop : -3.02 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 151 HIS 0.001 0.000 HIS A 143 PHE 0.015 0.001 PHE A 311 TYR 0.013 0.001 TYR B 123 ARG 0.001 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TRP cc_start: 0.8013 (m100) cc_final: 0.7795 (m100) REVERT: A 134 TYR cc_start: 0.7065 (t80) cc_final: 0.6847 (t80) REVERT: A 135 MET cc_start: 0.7156 (ttm) cc_final: 0.6385 (ttm) REVERT: A 136 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6434 (mm-30) REVERT: A 151 TRP cc_start: 0.7689 (m100) cc_final: 0.7139 (m100) REVERT: A 179 ILE cc_start: 0.8987 (mm) cc_final: 0.8532 (mt) REVERT: A 234 ARG cc_start: 0.6268 (ttm-80) cc_final: 0.5843 (mtt-85) REVERT: A 373 PHE cc_start: 0.8209 (t80) cc_final: 0.7918 (t80) REVERT: A 408 ILE cc_start: 0.8773 (mt) cc_final: 0.8554 (mt) REVERT: A 494 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6481 (mm-30) REVERT: A 553 ILE cc_start: 0.9053 (pt) cc_final: 0.8831 (pt) REVERT: C 47 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7393 (tm-30) REVERT: C 67 LEU cc_start: 0.6982 (mm) cc_final: 0.6741 (mm) REVERT: C 114 ILE cc_start: 0.8801 (pt) cc_final: 0.8581 (mp) REVERT: B 42 LYS cc_start: 0.6139 (mttt) cc_final: 0.5449 (tptt) REVERT: B 53 MET cc_start: 0.8867 (tpp) cc_final: 0.8515 (tpt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1767 time to fit residues: 48.3262 Evaluate side-chains 148 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 0.0070 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.0070 chunk 38 optimal weight: 0.0970 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6326 Z= 0.164 Angle : 0.595 9.667 8619 Z= 0.297 Chirality : 0.040 0.243 966 Planarity : 0.005 0.070 1048 Dihedral : 6.685 60.110 945 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.62 % Allowed : 16.00 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.30), residues: 758 helix: 0.14 (0.27), residues: 356 sheet: -2.62 (0.44), residues: 99 loop : -2.45 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 220 HIS 0.005 0.001 HIS C 111 PHE 0.018 0.001 PHE A 423 TYR 0.022 0.001 TYR B 123 ARG 0.004 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6596 (mm-30) REVERT: A 151 TRP cc_start: 0.7599 (m100) cc_final: 0.7007 (m100) REVERT: A 179 ILE cc_start: 0.8893 (mm) cc_final: 0.8576 (mt) REVERT: A 240 HIS cc_start: 0.7083 (p90) cc_final: 0.6596 (m170) REVERT: A 373 PHE cc_start: 0.8245 (t80) cc_final: 0.7875 (t80) REVERT: A 417 MET cc_start: 0.6044 (mtm) cc_final: 0.5496 (mtm) REVERT: A 494 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6567 (mm-30) REVERT: A 537 TRP cc_start: 0.8271 (m100) cc_final: 0.8045 (m-90) REVERT: A 553 ILE cc_start: 0.9112 (pt) cc_final: 0.8899 (pt) REVERT: B 42 LYS cc_start: 0.6294 (mttt) cc_final: 0.5784 (tptt) REVERT: B 53 MET cc_start: 0.9061 (tpp) cc_final: 0.8813 (tpt) REVERT: B 67 ILE cc_start: 0.7707 (mm) cc_final: 0.7473 (mm) REVERT: B 114 TYR cc_start: 0.8053 (m-80) cc_final: 0.7702 (m-80) outliers start: 17 outliers final: 9 residues processed: 171 average time/residue: 0.1685 time to fit residues: 39.0487 Evaluate side-chains 153 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6326 Z= 0.177 Angle : 0.595 11.124 8619 Z= 0.295 Chirality : 0.040 0.181 966 Planarity : 0.004 0.071 1048 Dihedral : 6.695 64.767 945 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.77 % Allowed : 20.00 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.49 (0.30), residues: 758 helix: 0.45 (0.28), residues: 351 sheet: -2.51 (0.43), residues: 101 loop : -2.12 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 55 HIS 0.005 0.001 HIS C 111 PHE 0.013 0.001 PHE A 133 TYR 0.021 0.001 TYR B 123 ARG 0.002 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6830 (mm-30) REVERT: A 151 TRP cc_start: 0.7680 (m100) cc_final: 0.7264 (m100) REVERT: A 393 ASP cc_start: 0.7538 (t0) cc_final: 0.7239 (t0) REVERT: A 417 MET cc_start: 0.5749 (mtm) cc_final: 0.5132 (mtm) REVERT: A 492 LEU cc_start: 0.8278 (mt) cc_final: 0.8004 (mt) REVERT: A 494 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6403 (mm-30) REVERT: A 553 ILE cc_start: 0.9166 (pt) cc_final: 0.8918 (pt) REVERT: B 42 LYS cc_start: 0.6278 (mttt) cc_final: 0.5753 (tptt) REVERT: B 67 ILE cc_start: 0.7755 (mm) cc_final: 0.7530 (mm) outliers start: 18 outliers final: 14 residues processed: 159 average time/residue: 0.1580 time to fit residues: 34.1076 Evaluate side-chains 155 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6326 Z= 0.162 Angle : 0.576 10.926 8619 Z= 0.286 Chirality : 0.039 0.160 966 Planarity : 0.004 0.070 1048 Dihedral : 6.486 62.415 945 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.08 % Allowed : 21.69 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.30 (0.30), residues: 758 helix: 0.45 (0.27), residues: 353 sheet: -2.23 (0.44), residues: 100 loop : -1.90 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 103 HIS 0.004 0.001 HIS C 111 PHE 0.010 0.001 PHE A 133 TYR 0.023 0.001 TYR A 134 ARG 0.005 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6980 (mm-30) REVERT: A 151 TRP cc_start: 0.7584 (m100) cc_final: 0.7126 (m100) REVERT: A 423 PHE cc_start: 0.8306 (m-80) cc_final: 0.8041 (m-10) REVERT: A 494 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6311 (mm-30) REVERT: A 553 ILE cc_start: 0.9190 (pt) cc_final: 0.8936 (pt) REVERT: B 42 LYS cc_start: 0.6072 (mttt) cc_final: 0.5717 (tptt) REVERT: B 58 GLN cc_start: 0.5813 (OUTLIER) cc_final: 0.5387 (tt0) REVERT: B 67 ILE cc_start: 0.7753 (mm) cc_final: 0.7550 (mm) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 0.1735 time to fit residues: 37.5629 Evaluate side-chains 155 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.0070 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6326 Z= 0.168 Angle : 0.581 11.269 8619 Z= 0.287 Chirality : 0.039 0.167 966 Planarity : 0.004 0.069 1048 Dihedral : 6.321 62.053 945 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.92 % Allowed : 24.15 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.18 (0.30), residues: 758 helix: 0.46 (0.27), residues: 356 sheet: -2.05 (0.45), residues: 100 loop : -1.80 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 103 HIS 0.004 0.001 HIS C 111 PHE 0.017 0.001 PHE A 428 TYR 0.020 0.001 TYR A 134 ARG 0.008 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6986 (mm-30) REVERT: A 151 TRP cc_start: 0.7573 (m100) cc_final: 0.7095 (m100) REVERT: A 240 HIS cc_start: 0.6982 (p90) cc_final: 0.6495 (m170) REVERT: A 494 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6297 (mm-30) REVERT: A 553 ILE cc_start: 0.9213 (pt) cc_final: 0.8956 (pt) REVERT: B 42 LYS cc_start: 0.6067 (mttt) cc_final: 0.5756 (tptt) REVERT: B 58 GLN cc_start: 0.5782 (OUTLIER) cc_final: 0.5504 (tt0) outliers start: 19 outliers final: 14 residues processed: 148 average time/residue: 0.1498 time to fit residues: 30.5847 Evaluate side-chains 151 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 0.2980 chunk 69 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6326 Z= 0.162 Angle : 0.576 9.810 8619 Z= 0.287 Chirality : 0.039 0.163 966 Planarity : 0.004 0.070 1048 Dihedral : 6.232 60.758 945 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.85 % Allowed : 24.15 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.08 (0.30), residues: 758 helix: 0.49 (0.27), residues: 358 sheet: -1.89 (0.46), residues: 100 loop : -1.72 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 103 HIS 0.004 0.001 HIS C 111 PHE 0.013 0.001 PHE A 428 TYR 0.020 0.001 TYR A 134 ARG 0.005 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6983 (mm-30) REVERT: A 151 TRP cc_start: 0.7609 (m100) cc_final: 0.7166 (m100) REVERT: A 240 HIS cc_start: 0.6982 (p90) cc_final: 0.6610 (m170) REVERT: A 370 MET cc_start: 0.6011 (mtt) cc_final: 0.5651 (mtt) REVERT: A 392 GLU cc_start: 0.4924 (OUTLIER) cc_final: 0.4618 (pt0) REVERT: A 494 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6292 (mm-30) REVERT: A 553 ILE cc_start: 0.9211 (pt) cc_final: 0.8948 (pt) REVERT: B 42 LYS cc_start: 0.6224 (mttt) cc_final: 0.5926 (tptt) REVERT: B 58 GLN cc_start: 0.5820 (OUTLIER) cc_final: 0.5103 (tt0) outliers start: 25 outliers final: 20 residues processed: 147 average time/residue: 0.1518 time to fit residues: 30.5267 Evaluate side-chains 155 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6326 Z= 0.192 Angle : 0.607 10.649 8619 Z= 0.299 Chirality : 0.040 0.145 966 Planarity : 0.004 0.070 1048 Dihedral : 6.293 60.391 945 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.69 % Allowed : 25.08 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.08 (0.30), residues: 758 helix: 0.49 (0.27), residues: 357 sheet: -1.89 (0.44), residues: 101 loop : -1.72 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 103 HIS 0.004 0.001 HIS C 111 PHE 0.018 0.001 PHE A 428 TYR 0.019 0.001 TYR B 123 ARG 0.008 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TRP cc_start: 0.6421 (p-90) cc_final: 0.6212 (p-90) REVERT: A 136 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7035 (mm-30) REVERT: A 151 TRP cc_start: 0.7693 (m100) cc_final: 0.7337 (m100) REVERT: A 240 HIS cc_start: 0.6987 (p90) cc_final: 0.6590 (m170) REVERT: A 494 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6321 (mm-30) REVERT: A 553 ILE cc_start: 0.9217 (pt) cc_final: 0.8951 (pt) REVERT: B 42 LYS cc_start: 0.6244 (mttt) cc_final: 0.5902 (tptt) REVERT: B 58 GLN cc_start: 0.5784 (OUTLIER) cc_final: 0.5080 (tt0) outliers start: 24 outliers final: 20 residues processed: 148 average time/residue: 0.1629 time to fit residues: 33.2193 Evaluate side-chains 154 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.0270 chunk 49 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6326 Z= 0.158 Angle : 0.601 11.569 8619 Z= 0.297 Chirality : 0.039 0.174 966 Planarity : 0.004 0.070 1048 Dihedral : 6.173 60.260 945 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.54 % Allowed : 25.08 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.98 (0.30), residues: 758 helix: 0.52 (0.27), residues: 356 sheet: -1.73 (0.46), residues: 101 loop : -1.62 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 55 HIS 0.003 0.001 HIS C 111 PHE 0.016 0.001 PHE A 311 TYR 0.020 0.001 TYR B 123 ARG 0.005 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6992 (mm-30) REVERT: A 151 TRP cc_start: 0.7522 (m100) cc_final: 0.7073 (m100) REVERT: A 240 HIS cc_start: 0.6957 (p90) cc_final: 0.6640 (m170) REVERT: A 370 MET cc_start: 0.5873 (mtt) cc_final: 0.5569 (mtt) REVERT: A 553 ILE cc_start: 0.9206 (pt) cc_final: 0.8937 (pt) REVERT: B 42 LYS cc_start: 0.6179 (mttt) cc_final: 0.5969 (tptt) REVERT: B 58 GLN cc_start: 0.5611 (OUTLIER) cc_final: 0.4854 (tt0) outliers start: 23 outliers final: 21 residues processed: 153 average time/residue: 0.1658 time to fit residues: 34.5513 Evaluate side-chains 155 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 123 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6326 Z= 0.172 Angle : 0.623 12.045 8619 Z= 0.308 Chirality : 0.040 0.194 966 Planarity : 0.004 0.071 1048 Dihedral : 6.125 60.121 945 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.38 % Allowed : 25.08 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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 (0.30), residues: 758 helix: 0.62 (0.27), residues: 350 sheet: -1.67 (0.48), residues: 96 loop : -1.60 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 55 HIS 0.002 0.001 HIS C 111 PHE 0.023 0.001 PHE A 428 TYR 0.019 0.001 TYR B 123 ARG 0.006 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6949 (mm-30) REVERT: A 151 TRP cc_start: 0.7552 (m100) cc_final: 0.7128 (m100) REVERT: A 240 HIS cc_start: 0.6980 (p90) cc_final: 0.6697 (m170) REVERT: A 370 MET cc_start: 0.5833 (mtt) cc_final: 0.5552 (mtt) REVERT: A 553 ILE cc_start: 0.9204 (pt) cc_final: 0.8937 (pt) REVERT: C 99 GLN cc_start: 0.6619 (mp10) cc_final: 0.6406 (mp10) REVERT: B 42 LYS cc_start: 0.6104 (mttt) cc_final: 0.5864 (tptt) REVERT: B 58 GLN cc_start: 0.5614 (OUTLIER) cc_final: 0.4845 (tt0) outliers start: 22 outliers final: 18 residues processed: 149 average time/residue: 0.1569 time to fit residues: 31.9961 Evaluate side-chains 157 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6326 Z= 0.177 Angle : 0.623 10.276 8619 Z= 0.309 Chirality : 0.040 0.209 966 Planarity : 0.004 0.071 1048 Dihedral : 6.074 59.466 945 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.23 % Allowed : 25.69 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.92 (0.30), residues: 758 helix: 0.57 (0.27), residues: 350 sheet: -1.80 (0.47), residues: 97 loop : -1.53 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 55 HIS 0.004 0.001 HIS C 111 PHE 0.021 0.001 PHE B 48 TYR 0.020 0.001 TYR B 123 ARG 0.005 0.000 ARG C 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7001 (mm-30) REVERT: A 151 TRP cc_start: 0.7587 (m100) cc_final: 0.7190 (m100) REVERT: A 240 HIS cc_start: 0.6967 (p90) cc_final: 0.6659 (m170) REVERT: A 370 MET cc_start: 0.5814 (mtt) cc_final: 0.5529 (mtt) REVERT: A 456 HIS cc_start: 0.6057 (p-80) cc_final: 0.5744 (p-80) REVERT: A 553 ILE cc_start: 0.9202 (pt) cc_final: 0.8933 (pt) REVERT: B 42 LYS cc_start: 0.5974 (mttt) cc_final: 0.5771 (tptt) outliers start: 21 outliers final: 17 residues processed: 150 average time/residue: 0.1532 time to fit residues: 31.5306 Evaluate side-chains 153 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.189699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.172669 restraints weight = 10157.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.176786 restraints weight = 6156.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.179566 restraints weight = 4174.379| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6326 Z= 0.181 Angle : 0.644 11.701 8619 Z= 0.316 Chirality : 0.042 0.375 966 Planarity : 0.004 0.071 1048 Dihedral : 6.028 59.341 945 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.92 % Allowed : 26.46 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.84 (0.30), residues: 758 helix: 0.65 (0.28), residues: 346 sheet: -1.65 (0.49), residues: 91 loop : -1.53 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 55 HIS 0.004 0.001 HIS C 111 PHE 0.017 0.001 PHE A 311 TYR 0.020 0.001 TYR B 123 ARG 0.005 0.000 ARG C 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.86 seconds wall clock time: 33 minutes 48.33 seconds (2028.33 seconds total)